data/jalview-2.7.dfsg/build.xml:208: uptodate ==> up-to-date
data/jalview-2.7.dfsg/doc/developing.html:26: whats ==> what's
data/jalview-2.7.dfsg/help/helpTOC.xml:126: nd ==> and, 2nd
data/jalview-2.7.dfsg/help/html/releases.html:294: keword ==> keyword
data/jalview-2.7.dfsg/help/html/releases.html:892: exisiting ==> existing
data/jalview-2.7.dfsg/help/html/memory.html:53: othewise ==> otherwise
data/jalview-2.7.dfsg/help/html/menus/popupMenu.html:34: Copys ==> Copies
data/jalview-2.7.dfsg/help/html/menus/popupMenu.html:65: decription ==> description
data/jalview-2.7.dfsg/help/html/menus/alignmentMenu.html:302: Seqence ==> Sequence
data/jalview-2.7.dfsg/help/html/menus/desktopMenu.html:105: browseable ==> browsable
data/jalview-2.7.dfsg/help/html/menus/alwview.html:72: Seqence ==> Sequence
data/jalview-2.7.dfsg/help/html/menus/alwannotations.html:49: avalable ==> available
data/jalview-2.7.dfsg/help/html/misc/aminoAcids.html:219: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/aminoAcids.html:230: ser ==> set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:55: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:55: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:55: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:55: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:74: Ser ==> Set
data/jalview-2.7.dfsg/help/html/misc/geneticCode.html:74: Ser ==> Set
data/jalview-2.7.dfsg/help/html/calculations/quality.html:44: substition ==> substitution
data/jalview-2.7.dfsg/help/html/webServices/webServicesPrefs.html:51: unwieldly ==> unwieldy
data/jalview-2.7.dfsg/help/html/webServices/dbreffetcher.html:49: identifaction ==> identification
data/jalview-2.7.dfsg/help/html/colourSchemes/clustal.html:43: Threshhold ==> Threshold
data/jalview-2.7.dfsg/help/html/features/featuresFormat.html:88: ommitted ==> omitted
data/jalview-2.7.dfsg/help/html/features/multipleViews.html:45: simultanously ==> simultaneously
data/jalview-2.7.dfsg/help/html/features/hiddenRegions.html:41: propogated ==> propagated
data/jalview-2.7.dfsg/help/html/features/groovy.html:73: environent ==> environment
data/jalview-2.7.dfsg/help/html/features/search.html:34: occurence ==> occurrence
data/jalview-2.7.dfsg/help/html/features/search.html:58: occurences ==> occurrences
data/jalview-2.7.dfsg/help/html/features/dassettings.html:43: buton ==> button
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das2/Das2SourceImpl.java:118: capabilitiy ==> capability
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das2/Das2Source.java:39: capabilties ==> capabilities
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/FeatureTrackImpl.java:34: segmetns ==> segments
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/FeatureTrackImpl.java:34: cotnains ==> contains
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java:30: diplayed ==> displayed
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java:141: methd ==> method
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java:143: methd ==> method
data/jalview-2.7.dfsg/src/org/biojava/dasobert/feature/FeatureTrack.java:59: methd ==> method
data/jalview-2.7.dfsg/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java:64: piority ==> priority
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:47: successfull ==> successful
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:172: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:173: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:175: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:189: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:190: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/FeatureThread.java:192: fiter ==> filter, fighter, fitter, fiver
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/SequenceThread.java:146: retreive ==> retrieve
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/SequenceThread.java:291: occured ==> occurred
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/DAS_Feature_Handler.java:89: emtpy ==> empty
data/jalview-2.7.dfsg/src/org/biojava/dasobert/das/DAS_Feature_Handler.java:120: maximium ==> maximum
data/jalview-2.7.dfsg/src/org/jibble/epsgraphics/EpsGraphics2D.java:67: accomodate ==> accommodate
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Replacer.java:71: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Replacer.java:107: occurences ==> occurrences
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Replacer.java:108: postition ==> position
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Replacer.java:224: preceeding ==> preceding, proceeding
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Pattern.java:32: interal ==> internal, interval, integral
data/jalview-2.7.dfsg/src/com/stevesoft/pat/SkipBMH.java:17: technic ==> technique
data/jalview-2.7.dfsg/src/com/stevesoft/pat/FileRegex.java:68: unitialized ==> uninitialized
data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegRes.java:183: backrefence ==> backreference
data/jalview-2.7.dfsg/src/com/stevesoft/pat/RegRes.java:193: preceeds ==> precedes, proceeds
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Range.java:18: Implments ==> Implements
data/jalview-2.7.dfsg/src/com/stevesoft/pat/StrPos.java:133: preceeded ==> preceded, proceeded
data/jalview-2.7.dfsg/src/com/stevesoft/pat/CaseMgr.java:16: accomodate ==> accommodate
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:512: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:525: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:538: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:551: occurences ==> occurrences
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:569: occurences ==> occurrences
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:582: occurences ==> occurrences
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:814: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:842: occurence ==> occurrence
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:1096: extentions ==> extensions
data/jalview-2.7.dfsg/src/com/stevesoft/pat/Regex.java:1962: occurences ==> occurrences
data/jalview-2.7.dfsg/src/vamsas/objects/simple/JpredResult_Helper.java:59: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/JpredResult_Helper.java:70: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/MsaResult_Helper.java:72: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/MsaResult_Helper.java:83: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Sequence_Helper.java:59: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Sequence_Helper.java:70: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Object_Helper.java:47: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Object_Helper.java:58: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Msfalignment_Helper.java:59: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Msfalignment_Helper.java:70: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Alignment_Helper.java:65: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Alignment_Helper.java:76: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Result_Helper.java:113: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Result_Helper.java:124: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Secstructpred_Helper.java:53: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/Secstructpred_Helper.java:64: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/SequenceSet_Helper.java:53: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/SequenceSet_Helper.java:64: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/WsJobId_Helper.java:59: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/WsJobId_Helper.java:70: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/SeqSearchResult_Helper.java:71: ser ==> set
data/jalview-2.7.dfsg/src/vamsas/objects/simple/SeqSearchResult_Helper.java:82: ser ==> set
data/jalview-2.7.dfsg/src/jalview/analysis/CrossRef.java:377: crossreference ==> cross-reference
data/jalview-2.7.dfsg/src/jalview/analysis/Finder.java:44: calles ==> calls
data/jalview-2.7.dfsg/src/jalview/analysis/Finder.java:202: thats ==> that's
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:109: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:385: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:391: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:445: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:451: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:467: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:473: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:483: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:489: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:852: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:855: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/AlignSeq.java:860: defInt ==> definite, define
data/jalview-2.7.dfsg/src/jalview/analysis/SequenceIdMatcher.java:269: arbritrarily ==> arbitrarily
data/jalview-2.7.dfsg/src/jalview/analysis/AlignmentSorter.java:277: ORIGNAL ==> ORIGINAL
data/jalview-2.7.dfsg/src/jalview/analysis/Conservation.java:511: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/analysis/Dna.java:454: resSize ==> resize
data/jalview-2.7.dfsg/src/jalview/analysis/Dna.java:511: resSize ==> resize
data/jalview-2.7.dfsg/src/jalview/analysis/Dna.java:560: resSize ==> resize
data/jalview-2.7.dfsg/src/jalview/analysis/Dna.java:631: resSize ==> resize
data/jalview-2.7.dfsg/src/jalview/util/MapList.java:753: fromS ==> forms
data/jalview-2.7.dfsg/src/jalview/util/MapList.java:754: fromE ==> from
data/jalview-2.7.dfsg/src/jalview/util/MapList.java:756: fromS ==> forms
data/jalview-2.7.dfsg/src/jalview/util/MapList.java:756: fromE ==> from
data/jalview-2.7.dfsg/src/jalview/util/DBRefUtils.java:401: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/util/DBRefUtils.java:407: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/util/DBRefUtils.java:419: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/util/DBRefUtils.java:439: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/util/BrowserLauncher.java:61: repsonsible ==> responsible
data/jalview-2.7.dfsg/src/jalview/util/BrowserLauncher.java:307: intialization ==> initialization
data/jalview-2.7.dfsg/src/jalview/util/AWTConsole.java:26: Permision ==> Permission
data/jalview-2.7.dfsg/src/jalview/util/AWTConsole.java:109: seperate ==> separate
data/jalview-2.7.dfsg/src/jalview/util/AWTConsole.java:131: seperate ==> separate
data/jalview-2.7.dfsg/src/jalview/util/AWTConsole.java:131: becasue ==> because
data/jalview-2.7.dfsg/src/jalview/util/AWTConsole.java:131: wan't ==> want, wasn't
data/jalview-2.7.dfsg/src/jalview/util/GroupUrlLink.java:58: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/util/TableSorter.java:40: recieved ==> received
data/jalview-2.7.dfsg/src/jalview/util/TableSorter.java:514: succesive ==> successive
data/jalview-2.7.dfsg/src/jalview/schemes/GraduatedColor.java:274: appropriatly ==> appropriately
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:166: SER ==> SET
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:214: SER ==> SET
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:215: SER ==> SET
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:571: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:605: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:740: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:741: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:742: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:743: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:744: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/schemes/ResidueProperties.java:745: Ser ==> Set
data/jalview-2.7.dfsg/src/jalview/javascript/JalviewLiteJsApi.java:102: currrent ==> current
data/jalview-2.7.dfsg/src/jalview/javascript/JalviewLiteJsApi.java:113: currrent ==> current
data/jalview-2.7.dfsg/src/jalview/javascript/JalviewLiteJsApi.java:131: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/javascript/JalviewLiteJsApi.java:143: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/structure/StructureSelectionManager.java:418: sequeence ==> sequence
data/jalview-2.7.dfsg/src/jalview/structure/StructureSelectionManager.java:418: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/structure/StructureSelectionManager.java:487: seqeunce ==> sequence
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:78: continous ==> continuous
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:123: syncrhonized ==> synchronized
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:1212: continous ==> continuous
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:1637: datset ==> dataset
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:2012: cant ==> can't
data/jalview-2.7.dfsg/src/jalview/io/VamsasAppDatastore.java:2234: Unamed ==> Unnamed
data/jalview-2.7.dfsg/src/jalview/io/ModellerDescription.java:389: modifed ==> modified
data/jalview-2.7.dfsg/src/jalview/io/WSWUBlastClient.java:60: nIn ==> inn, min, bin, nine
data/jalview-2.7.dfsg/src/jalview/io/AppletFormatAdapter.java:520: Couln't ==> Couldn't
data/jalview-2.7.dfsg/src/jalview/io/MSFfile.java:105: seqeunce ==> sequence
data/jalview-2.7.dfsg/src/jalview/io/NewickFile.java:40: ND ==> AND, 2ND
data/jalview-2.7.dfsg/src/jalview/io/NewickFile.java:698: specificied ==> specified
data/jalview-2.7.dfsg/src/jalview/io/StockholmFile.java:100: regularily ==> regularly
data/jalview-2.7.dfsg/src/jalview/io/StockholmFile.java:170: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/io/StockholmFile.java:171: acn ==> can, acne
data/jalview-2.7.dfsg/src/jalview/io/StockholmFile.java:215: seqeunce ==> sequence
data/jalview-2.7.dfsg/src/jalview/io/FeaturesFile.java:177: theres ==> there's
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Tree.java:444: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Tree.java:449: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Tree.java:459: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:431: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:432: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:434: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:435: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:437: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:443: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:443: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:446: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/Sequencemapping.java:446: te ==> the, be, we
data/jalview-2.7.dfsg/src/jalview/io/vamsas/LocalDocSyncObject.java:45: opreations ==> operations
data/jalview-2.7.dfsg/src/jalview/ws/WSClient.java:34: Aligment ==> Alignment
data/jalview-2.7.dfsg/src/jalview/ws/EnfinEnvision2OneWay.java:470: selecton ==> selection
data/jalview-2.7.dfsg/src/jalview/ws/EnfinEnvision2OneWay.java:606: menues ==> menus
data/jalview-2.7.dfsg/src/jalview/ws/EnfinEnvision2OneWay.java:608: menues ==> menus
data/jalview-2.7.dfsg/src/jalview/ws/EnfinEnvision2OneWay.java:609: menues ==> menus
data/jalview-2.7.dfsg/src/jalview/ws/seqfetcher/DbSourceProxy.java:118: reponse ==> response
data/jalview-2.7.dfsg/src/jalview/ws/seqfetcher/ASequenceFetcher.java:309: Implmentation ==> Implementation
data/jalview-2.7.dfsg/src/jalview/ws/jws2/MsaWSThread.java:290: appropriatly ==> appropriately
data/jalview-2.7.dfsg/src/jalview/ws/jws2/MsaWSThread.java:379: progess ==> progress
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/Parameter.java:31: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/Parameter.java:33: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/IntegerParameter.java:69: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/IntegerParameter.java:71: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/IntegerParameter.java:72: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/params/simple/IntegerParameter.java:73: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJob.java:358: modifed ==> modified
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:609: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:630: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:643: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:644: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:651: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:666: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:719: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:724: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:726: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:759: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:770: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:771: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:784: alo ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:785: alo ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:787: alo ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:958: referemce ==> reference
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1018: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1025: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1028: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1040: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1051: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1052: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestJobThread.java:1101: als ==> also
data/jalview-2.7.dfsg/src/jalview/ws/rest/RestServiceDescription.java:281: ths ==> the, this
data/jalview-2.7.dfsg/src/jalview/ws/jws1/SeqSearchWSClient.java:134: earch ==> search, each
data/jalview-2.7.dfsg/src/jalview/ws/jws1/SeqSearchWSThread.java:266: appropriatly ==> appropriately
data/jalview-2.7.dfsg/src/jalview/ws/jws1/Discoverer.java:362: Curent ==> Current
data/jalview-2.7.dfsg/src/jalview/ws/jws1/JPredClient.java:35: crate ==> create
data/jalview-2.7.dfsg/src/jalview/ws/jws1/MsaWSThread.java:252: appropriatly ==> appropriately
data/jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java:283: ded ==> dead
data/jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java:296: ded ==> dead
data/jalview-2.7.dfsg/src/jalview/ext/jmol/JalviewJmolBinding.java:1300: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/jbgui/GAlignFrame.java:1477: visiblity ==> visibility
data/jalview-2.7.dfsg/src/jalview/jbgui/GAlignFrame.java:1486: visiblity ==> visibility
data/jalview-2.7.dfsg/src/jalview/jbgui/GAlignFrame.java:1496: visiblity ==> visibility
data/jalview-2.7.dfsg/src/jalview/jbgui/GAlignFrame.java:1505: visiblity ==> visibility
data/jalview-2.7.dfsg/src/jalview/gui/VamsasApplication.java:265: Impementation ==> Implementation
data/jalview-2.7.dfsg/src/jalview/gui/PCAPanel.java:279: alignmnt ==> alignment
data/jalview-2.7.dfsg/src/jalview/gui/WsJobParameters.java:94: non-existant ==> non-existent
data/jalview-2.7.dfsg/src/jalview/gui/WsJobParameters.java:99: modifed ==> modified
data/jalview-2.7.dfsg/src/jalview/gui/WsJobParameters.java:565: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/WsJobParameters.java:566: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/WsJobParameters.java:1243: modifed ==> modified
data/jalview-2.7.dfsg/src/jalview/gui/DasSourceBrowser.java:674: fo ==> of, for
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:287: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:290: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:291: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:292: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:307: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:311: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:316: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:324: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:325: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:330: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:336: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:337: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:341: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:344: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:367: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:368: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:405: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:410: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:411: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:423: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:549: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:596: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:602: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:609: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:611: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:616: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:873: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:874: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/OptsAndParamsPage.java:876: parm ==> param, pram, parma
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:28: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:264: exisiting ==> existing
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:280: initalise ==> initialise
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1291: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1291: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1304: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1304: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1314: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1336: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1339: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1341: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1361: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1361: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1391: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1391: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:1408: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:3587: curent ==> current
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4222: ths ==> the, this
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4230: ths ==> the, this
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4233: ths ==> the, this
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4275: crossreferences ==> cross-references
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4278: crossreferences ==> cross-references
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4281: crossreferences ==> cross-references
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4284: ths ==> the, this
data/jalview-2.7.dfsg/src/jalview/gui/AlignFrame.java:4386: corectly ==> correctly
data/jalview-2.7.dfsg/src/jalview/gui/RedundancyPanel.java:43: synching ==> syncing
data/jalview-2.7.dfsg/src/jalview/gui/RedundancyPanel.java:306: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/RedundancyPanel.java:306: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/UserQuestionnaireCheck.java:57: responsed ==> responded, responses
data/jalview-2.7.dfsg/src/jalview/gui/UserQuestionnaireCheck.java:99: wee ==> we
data/jalview-2.7.dfsg/src/jalview/gui/UserQuestionnaireCheck.java:125: responsed ==> responded, responses
data/jalview-2.7.dfsg/src/jalview/gui/PromptUserConfig.java:128: wee ==> we
data/jalview-2.7.dfsg/src/jalview/gui/AssociatePdbFileWithSeq.java:35: assocate ==> associate
data/jalview-2.7.dfsg/src/jalview/gui/Desktop.java:1629: fle ==> file
data/jalview-2.7.dfsg/src/jalview/gui/Desktop.java:1633: fle ==> file
data/jalview-2.7.dfsg/src/jalview/gui/Desktop.java:2424: nin ==> inn, min, bin, nine
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:673: dout ==> doubt
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:674: dout ==> doubt
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:675: dout ==> doubt
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:2127: visiblity ==> visibility
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:2651: nin ==> inn, min, bin, nine
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:2651: nIn ==> inn, min, bin, nine
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3185: featre ==> feature
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3261: aready ==> already
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3865: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3866: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3870: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3872: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3875: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Jalview2XML.java:3877: anid ==> and
data/jalview-2.7.dfsg/src/jalview/gui/Console.java:32: Permision ==> Permission
data/jalview-2.7.dfsg/src/jalview/gui/Console.java:115: seperate ==> separate
data/jalview-2.7.dfsg/src/jalview/gui/Console.java:229: seperate ==> separate
data/jalview-2.7.dfsg/src/jalview/gui/Console.java:229: becasue ==> because
data/jalview-2.7.dfsg/src/jalview/gui/Console.java:229: wan't ==> want, wasn't
data/jalview-2.7.dfsg/src/jalview/gui/PopupMenu.java:592: selecton ==> selection
data/jalview-2.7.dfsg/src/jalview/gui/FeatureRenderer.java:416: retreived ==> retrieved
data/jalview-2.7.dfsg/src/jalview/gui/FeatureRenderer.java:653: immediatly ==> immediately
data/jalview-2.7.dfsg/src/jalview/gui/FeatureRenderer.java:1382: theses ==> these, thesis
data/jalview-2.7.dfsg/src/jalview/gui/SeqPanel.java:1365: theres ==> there's
data/jalview-2.7.dfsg/src/jalview/gui/SeqPanel.java:1371: Theres ==> There's
data/jalview-2.7.dfsg/src/jalview/gui/SeqPanel.java:1908: immediatly ==> immediately
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:32: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:444: alignmnt ==> alignment
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:515: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:515: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:521: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:527: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:549: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:566: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/TreePanel.java:571: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/gui/SequenceFetcher.java:110: occuring ==> occurring
data/jalview-2.7.dfsg/src/jalview/gui/SequenceFetcher.java:435: anthing ==> anything
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:267: exisiting ==> existing
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:567: exisiting ==> existing
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:698: successfuly ==> successfully
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:1250: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:1257: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/AppJmol.java:1261: als ==> also
data/jalview-2.7.dfsg/src/jalview/gui/TreeCanvas.java:810: ect ==> etc
data/jalview-2.7.dfsg/src/jalview/gui/OOMWarning.java:36: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/commands/ChangeCaseCommand.java:22: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/commands/OrderCommand.java:23: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/commands/EditCommand.java:46: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/commands/CommandI.java:20: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/datamodel/Mapping.java:349: modifed ==> modified
data/jalview-2.7.dfsg/src/jalview/datamodel/CigarBase.java:193: formated ==> formatted
data/jalview-2.7.dfsg/src/jalview/datamodel/CigarBase.java:318: aligment ==> alignment
data/jalview-2.7.dfsg/src/jalview/datamodel/SequenceNode.java:112: refered ==> referred
data/jalview-2.7.dfsg/src/jalview/datamodel/AlignedCodonFrame.java:39: alignement ==> alignment
data/jalview-2.7.dfsg/src/jalview/datamodel/SequenceGroup.java:443: aligment ==> alignment
data/jalview-2.7.dfsg/src/jalview/datamodel/CigarArray.java:295: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/datamodel/CigarArray.java:296: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/datamodel/SeqCigar.java:500: diffferent ==> different
data/jalview-2.7.dfsg/src/jalview/datamodel/SeqCigar.java:563: incorect ==> incorrect
data/jalview-2.7.dfsg/src/jalview/datamodel/AlignmentView.java:734: begining ==> beginning
data/jalview-2.7.dfsg/src/jalview/datamodel/SequenceI.java:290: doesnt ==> doesn't, does not
data/jalview-2.7.dfsg/src/jalview/datamodel/Sequence.java:498: seqeunce ==> sequence
data/jalview-2.7.dfsg/src/jalview/datamodel/Sequence.java:750: occured ==> occurred
data/jalview-2.7.dfsg/src/jalview/datamodel/xdb/embl/EmblEntry.java:639: trunctation ==> truncation
data/jalview-2.7.dfsg/src/jalview/appletgui/PCAPanel.java:223: alignmnt ==> alignment
data/jalview-2.7.dfsg/src/jalview/appletgui/AnnotationLabels.java:248: curent ==> current
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:136: Havent ==> Haven't
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1212: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1212: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1225: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1225: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1235: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1259: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1259: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1284: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1284: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1296: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:1540: preceeding ==> preceding, proceeding
data/jalview-2.7.dfsg/src/jalview/appletgui/AlignFrame.java:3264: Seperator ==> Separator
data/jalview-2.7.dfsg/src/jalview/appletgui/ExtJmol.java:153: overriden ==> overridden
data/jalview-2.7.dfsg/src/jalview/appletgui/RedundancyPanel.java:33: synching ==> syncing
data/jalview-2.7.dfsg/src/jalview/appletgui/RedundancyPanel.java:268: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/RedundancyPanel.java:268: CommandI ==> command
data/jalview-2.7.dfsg/src/jalview/appletgui/FeatureRenderer.java:961: theses ==> these, thesis
data/jalview-2.7.dfsg/src/jalview/appletgui/SeqPanel.java:1247: theres ==> there's
data/jalview-2.7.dfsg/src/jalview/appletgui/SeqPanel.java:1253: Theres ==> There's
data/jalview-2.7.dfsg/src/jalview/appletgui/SeqPanel.java:1723: immediatly ==> immediately
data/jalview-2.7.dfsg/src/jalview/appletgui/SliderPanel.java:177: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/appletgui/TreePanel.java:138: alignmnt ==> alignment
data/jalview-2.7.dfsg/src/jalview/appletgui/TreeCanvas.java:517: ect ==> etc
data/jalview-2.7.dfsg/src/jalview/schemabinding/version2/Features.java:112: Featur ==> Feature
data/jalview-2.7.dfsg/src/jalview/schemabinding/version2/Feature.java:515: Featur ==> Feature
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:220: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:231: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:237: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:240: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:242: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:248: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:251: selectIn ==> selection, selecting
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:1831: Successfuly ==> Successfully
data/jalview-2.7.dfsg/src/jalview/bin/JalviewLite.java:2421: paremeter ==> parameter
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:98: tRun ==> turn
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:100: tThe ==> the
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:146: overriden ==> overridden
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:265: Exeption ==> Exception, exemption
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:905: occurence ==> occurrence
data/jalview-2.7.dfsg/src/jalview/bin/Jalview.java:940: occurence ==> occurrence
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry_Helper.java:49: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry_Helper.java:57: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry_Helper.java:91: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry_Helper.java:102: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference_Helper.java:24: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference_Helper.java:29: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference_Helper.java:110: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference_Helper.java:121: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:26: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:28: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:39: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:40: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:96: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:107: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:112: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:119: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:129: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:140: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:145: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/UPEntry.java:151: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:20: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:40: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:44: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:63: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:73: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:83: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:93: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:103: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:113: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:123: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:133: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:143: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:153: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:163: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:173: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:183: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:193: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:203: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:213: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:223: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:233: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:246: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:248: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/picr/model/CrossReference.java:248: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/InputParams.java:451: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/InputParams.java:462: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSFile.java:139: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSFile.java:150: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:56: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:57: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:58: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:59: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:60: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:61: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:62: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java:63: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/Data.java:139: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/Data.java:150: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:161: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:162: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:163: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:164: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:165: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:166: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:167: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:168: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:169: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:170: ser ==> set
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:180: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java:182: CrossReference ==> cross-reference
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:130: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:131: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:134: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:135: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:137: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:139: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:141: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:143: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:145: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/JpredSoapBindingStub.java:147: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/ServiceHandle.java:239: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/ServiceHandle.java:250: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:65: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:66: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:68: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:70: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:71: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:72: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:74: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:76: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:78: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/MuscleWSSoapBindingStub.java:80: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/ServiceHandles.java:139: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/ServiceHandles.java:150: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:80: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:81: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:83: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:85: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:86: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:87: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:89: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:91: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:93: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/RegistryServiceSoapBindingStub.java:95: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:148: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:149: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:150: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:151: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:152: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:153: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:154: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:155: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:156: ser ==> set
data/jalview-2.7.dfsg/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java:157: ser ==> set
data/jalview-2.7.dfsg/debian/manpages/jalview.1:8: alignement ==> alignment
data/jalview-2.7.dfsg/.pc/mutilate-build-system.diff/build.xml:219: uptodate ==> up-to-date
data/jalview-2.7.dfsg/.pc/newer-jmol-api.diff/build.xml:208: uptodate ==> up-to-date
data/jalview-2.7.dfsg/.pc/newer-jmol-api.diff/src/jalview/ext/jmol/JalviewJmolBinding.java:275: ded ==> dead
data/jalview-2.7.dfsg/.pc/newer-jmol-api.diff/src/jalview/ext/jmol/JalviewJmolBinding.java:288: ded ==> dead
data/jalview-2.7.dfsg/.pc/newer-jmol-api.diff/src/jalview/ext/jmol/JalviewJmolBinding.java:1290: occured ==> occurred