[med-svn] [mesquite] 03/05: Merge tag 'upstream/3.04+dfsg.1'
Andreas Tille
tille at debian.org
Mon May 23 13:47:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mesquite.
commit 74805ab9286db6477dfa21fdb93a7c1768b1abb2
Merge: d96219a ca7b9fe
Author: Andreas Tille <tille at debian.org>
Date: Mon May 23 10:26:31 2016 +0200
Merge tag 'upstream/3.04+dfsg.1'
Upstream version 3.04+dfsg.1
LibrarySource/com/lowagie/text/Anchor.java | 366 ---
LibrarySource/com/lowagie/text/Annotation.java | 727 -----
.../com/lowagie/text/BadElementException.java | 89 -
LibrarySource/com/lowagie/text/Cell.java | 1006 -------
LibrarySource/com/lowagie/text/Chapter.java | 156 -
LibrarySource/com/lowagie/text/Chunk.java | 788 -----
LibrarySource/com/lowagie/text/DocListener.java | 182 --
LibrarySource/com/lowagie/text/DocWriter.java | 510 ----
LibrarySource/com/lowagie/text/Document.java | 916 ------
.../com/lowagie/text/DocumentException.java | 186 --
LibrarySource/com/lowagie/text/Element.java | 319 --
.../com/lowagie/text/ElementListener.java | 75 -
LibrarySource/com/lowagie/text/ElementTags.java | 461 ---
LibrarySource/com/lowagie/text/Entities.java | 388 ---
.../com/lowagie/text/ExceptionConverter.java | 135 -
LibrarySource/com/lowagie/text/Font.java | 752 -----
LibrarySource/com/lowagie/text/FontFactory.java | 661 -----
LibrarySource/com/lowagie/text/Graphic.java | 277 --
LibrarySource/com/lowagie/text/GreekList.java | 141 -
LibrarySource/com/lowagie/text/Header.java | 98 -
LibrarySource/com/lowagie/text/HeaderFooter.java | 206 --
LibrarySource/com/lowagie/text/Image.java | 1892 ------------
LibrarySource/com/lowagie/text/ImgCCITT.java | 146 -
LibrarySource/com/lowagie/text/ImgPostscript.java | 220 --
LibrarySource/com/lowagie/text/ImgRaw.java | 97 -
LibrarySource/com/lowagie/text/ImgTemplate.java | 91 -
LibrarySource/com/lowagie/text/ImgWMF.java | 190 --
LibrarySource/com/lowagie/text/Jpeg.java | 350 ---
LibrarySource/com/lowagie/text/List.java | 549 ----
LibrarySource/com/lowagie/text/ListItem.java | 292 --
.../com/lowagie/text/MarkupAttributes.java | 102 -
LibrarySource/com/lowagie/text/Meta.java | 263 --
LibrarySource/com/lowagie/text/PageSize.java | 153 -
LibrarySource/com/lowagie/text/Paragraph.java | 517 ----
LibrarySource/com/lowagie/text/Phrase.java | 595 ----
LibrarySource/com/lowagie/text/Rectangle.java | 869 ------
LibrarySource/com/lowagie/text/RomanList.java | 291 --
LibrarySource/com/lowagie/text/Row.java | 470 ---
LibrarySource/com/lowagie/text/Section.java | 660 -----
LibrarySource/com/lowagie/text/SpecialSymbol.java | 214 --
LibrarySource/com/lowagie/text/SplitCharacter.java | 99 -
LibrarySource/com/lowagie/text/StringCompare.java | 77 -
LibrarySource/com/lowagie/text/Table.java | 1952 -------------
.../com/lowagie/text/TextElementArray.java | 75 -
LibrarySource/com/lowagie/text/Watermark.java | 123 -
.../com/lowagie/text/ZapfDingbatsList.java | 119 -
.../com/lowagie/text/ZapfDingbatsNumberList.java | 132 -
.../com/lowagie/text/html/HtmlEncoder.java | 211 --
LibrarySource/com/lowagie/text/html/HtmlTags.java | 331 ---
.../com/lowagie/text/html/HtmlWriter.java | 1084 -------
.../text/html/simpleparser/ChainedProperties.java | 127 -
.../text/html/simpleparser/FactoryProperties.java | 174 --
.../lowagie/text/html/simpleparser/HTMLWorker.java | 500 ----
.../lowagie/text/html/simpleparser/IncCell.java | 124 -
.../lowagie/text/html/simpleparser/IncTable.java | 122 -
.../lowagie/text/html/simpleparser/StyleSheet.java | 112 -
.../com/lowagie/text/markup/MarkupParser.java | 567 ----
.../com/lowagie/text/markup/MarkupTags.java | 233 --
.../com/lowagie/text/pdf/ArabicLigaturizer.java | 772 -----
.../com/lowagie/text/pdf/AsianFontMapper.java | 104 -
.../lowagie/text/pdf/BadPdfFormatException.java | 86 -
LibrarySource/com/lowagie/text/pdf/BaseField.java | 686 -----
LibrarySource/com/lowagie/text/pdf/BaseFont.java | 1094 -------
LibrarySource/com/lowagie/text/pdf/BidiLine.java | 915 ------
LibrarySource/com/lowagie/text/pdf/BidiOrder.java | 1241 --------
LibrarySource/com/lowagie/text/pdf/ByteBuffer.java | 597 ----
LibrarySource/com/lowagie/text/pdf/CFFFont.java | 1184 --------
.../com/lowagie/text/pdf/CFFFontSubset.java | 1633 -----------
LibrarySource/com/lowagie/text/pdf/CJKFont.java | 626 ----
LibrarySource/com/lowagie/text/pdf/CMYKColor.java | 118 -
.../com/lowagie/text/pdf/ColorDetails.java | 102 -
LibrarySource/com/lowagie/text/pdf/ColumnText.java | 1420 ---------
.../com/lowagie/text/pdf/DefaultFontMapper.java | 309 --
.../com/lowagie/text/pdf/DocumentFont.java | 413 ---
.../com/lowagie/text/pdf/EnumerateTTC.java | 119 -
.../com/lowagie/text/pdf/ExtendedColor.java | 122 -
.../com/lowagie/text/pdf/ExtraEncoding.java | 74 -
LibrarySource/com/lowagie/text/pdf/FdfReader.java | 214 --
.../com/lowagie/text/pdf/FontDetails.java | 279 --
LibrarySource/com/lowagie/text/pdf/FontMapper.java | 81 -
.../com/lowagie/text/pdf/FontSelector.java | 124 -
LibrarySource/com/lowagie/text/pdf/GlyphList.java | 2200 --------------
LibrarySource/com/lowagie/text/pdf/GrayColor.java | 75 -
.../com/lowagie/text/pdf/HyphenationAuto.java | 126 -
.../com/lowagie/text/pdf/HyphenationEvent.java | 79 -
.../com/lowagie/text/pdf/IntHashtable.java | 339 ---
LibrarySource/com/lowagie/text/pdf/LZWDecoder.java | 232 --
.../com/lowagie/text/pdf/MultiColumnText.java | 504 ----
.../com/lowagie/text/pdf/OutputStreamCounter.java | 170 --
.../com/lowagie/text/pdf/PRIndirectReference.java | 103 -
LibrarySource/com/lowagie/text/pdf/PRStream.java | 229 --
.../com/lowagie/text/pdf/PRTokeniser.java | 587 ----
.../com/lowagie/text/pdf/PageResources.java | 175 --
.../com/lowagie/text/pdf/PatternColor.java | 71 -
.../com/lowagie/text/pdf/PdfAcroForm.java | 744 -----
LibrarySource/com/lowagie/text/pdf/PdfAction.java | 558 ----
.../com/lowagie/text/pdf/PdfAnnotation.java | 741 -----
.../com/lowagie/text/pdf/PdfAppearance.java | 151 -
LibrarySource/com/lowagie/text/pdf/PdfArray.java | 223 --
LibrarySource/com/lowagie/text/pdf/PdfBoolean.java | 130 -
.../com/lowagie/text/pdf/PdfBorderArray.java | 82 -
.../com/lowagie/text/pdf/PdfBorderDictionary.java | 100 -
LibrarySource/com/lowagie/text/pdf/PdfCell.java | 883 ------
LibrarySource/com/lowagie/text/pdf/PdfChunk.java | 782 -----
LibrarySource/com/lowagie/text/pdf/PdfColor.java | 80 -
.../com/lowagie/text/pdf/PdfContentByte.java | 2728 -----------------
.../com/lowagie/text/pdf/PdfContents.java | 147 -
.../com/lowagie/text/pdf/PdfDashPattern.java | 144 -
LibrarySource/com/lowagie/text/pdf/PdfDate.java | 190 --
.../com/lowagie/text/pdf/PdfDestination.java | 221 --
.../com/lowagie/text/pdf/PdfDictionary.java | 315 --
.../com/lowagie/text/pdf/PdfDocument.java | 2972 -------------------
.../com/lowagie/text/pdf/PdfEncodings.java | 717 -----
.../com/lowagie/text/pdf/PdfEncryption.java | 363 ---
.../com/lowagie/text/pdf/PdfEncryptionStream.java | 85 -
.../com/lowagie/text/pdf/PdfException.java | 86 -
.../com/lowagie/text/pdf/PdfFileSpecification.java | 188 --
LibrarySource/com/lowagie/text/pdf/PdfFont.java | 189 --
.../com/lowagie/text/pdf/PdfFormField.java | 353 ---
.../com/lowagie/text/pdf/PdfFormXObject.java | 105 -
.../com/lowagie/text/pdf/PdfFunction.java | 143 -
LibrarySource/com/lowagie/text/pdf/PdfGState.java | 144 -
.../com/lowagie/text/pdf/PdfGraphics2D.java | 1423 ---------
.../com/lowagie/text/pdf/PdfICCBased.java | 88 -
LibrarySource/com/lowagie/text/pdf/PdfImage.java | 281 --
.../com/lowagie/text/pdf/PdfImportedPage.java | 150 -
.../com/lowagie/text/pdf/PdfIndirectObject.java | 171 --
.../com/lowagie/text/pdf/PdfIndirectReference.java | 129 -
LibrarySource/com/lowagie/text/pdf/PdfLayer.java | 302 --
.../com/lowagie/text/pdf/PdfLayerMembership.java | 140 -
LibrarySource/com/lowagie/text/pdf/PdfLine.java | 476 ---
LibrarySource/com/lowagie/text/pdf/PdfLister.java | 187 --
LibrarySource/com/lowagie/text/pdf/PdfLiteral.java | 111 -
.../com/lowagie/text/pdf/PdfMediaClipData.java | 64 -
LibrarySource/com/lowagie/text/pdf/PdfName.java | 1093 -------
.../com/lowagie/text/pdf/PdfNameTree.java | 165 --
LibrarySource/com/lowagie/text/pdf/PdfNull.java | 83 -
LibrarySource/com/lowagie/text/pdf/PdfNumber.java | 159 -
LibrarySource/com/lowagie/text/pdf/PdfOCG.java | 67 -
.../com/lowagie/text/pdf/PdfOCProperties.java | 59 -
LibrarySource/com/lowagie/text/pdf/PdfObject.java | 371 ---
LibrarySource/com/lowagie/text/pdf/PdfOutline.java | 542 ----
LibrarySource/com/lowagie/text/pdf/PdfPCell.java | 697 -----
.../com/lowagie/text/pdf/PdfPCellEvent.java | 74 -
LibrarySource/com/lowagie/text/pdf/PdfPRow.java | 530 ----
.../com/lowagie/text/pdf/PdfPSXObject.java | 99 -
LibrarySource/com/lowagie/text/pdf/PdfPTable.java | 1014 -------
.../com/lowagie/text/pdf/PdfPTableEvent.java | 95 -
LibrarySource/com/lowagie/text/pdf/PdfPage.java | 198 --
.../com/lowagie/text/pdf/PdfPageElement.java | 78 -
.../com/lowagie/text/pdf/PdfPageEvent.java | 191 --
.../com/lowagie/text/pdf/PdfPageEventHelper.java | 203 --
.../com/lowagie/text/pdf/PdfPageLabels.java | 192 --
LibrarySource/com/lowagie/text/pdf/PdfPages.java | 206 --
LibrarySource/com/lowagie/text/pdf/PdfPattern.java | 84 -
.../com/lowagie/text/pdf/PdfPatternPainter.java | 391 ---
.../com/lowagie/text/pdf/PdfPrinterGraphics2D.java | 73 -
LibrarySource/com/lowagie/text/pdf/PdfReader.java | 3052 --------------------
.../com/lowagie/text/pdf/PdfReaderInstance.java | 183 --
.../com/lowagie/text/pdf/PdfRectangle.java | 277 --
.../com/lowagie/text/pdf/PdfRendition.java | 62 -
.../com/lowagie/text/pdf/PdfResources.java | 91 -
LibrarySource/com/lowagie/text/pdf/PdfShading.java | 262 --
.../com/lowagie/text/pdf/PdfShadingPattern.java | 120 -
.../com/lowagie/text/pdf/PdfSpotColor.java | 132 -
LibrarySource/com/lowagie/text/pdf/PdfStream.java | 287 --
LibrarySource/com/lowagie/text/pdf/PdfString.java | 236 --
LibrarySource/com/lowagie/text/pdf/PdfTable.java | 316 --
.../com/lowagie/text/pdf/PdfTemplate.java | 267 --
.../com/lowagie/text/pdf/PdfTextArray.java | 99 -
.../com/lowagie/text/pdf/PdfTransition.java | 253 --
.../com/lowagie/text/pdf/PdfTransparencyGroup.java | 85 -
LibrarySource/com/lowagie/text/pdf/PdfWriter.java | 2542 ----------------
.../lowagie/text/pdf/PdfXConformanceException.java | 70 -
LibrarySource/com/lowagie/text/pdf/Pfm2afm.java | 774 -----
.../com/lowagie/text/pdf/PushbuttonField.java | 602 ----
.../com/lowagie/text/pdf/RadioCheckField.java | 416 ---
.../lowagie/text/pdf/RandomAccessFileOrArray.java | 594 ----
.../com/lowagie/text/pdf/SequenceList.java | 316 --
.../com/lowagie/text/pdf/ShadingColor.java | 75 -
.../com/lowagie/text/pdf/SimpleBookmark.java | 745 -----
.../lowagie/text/pdf/SimpleNamedDestination.java | 335 ---
.../com/lowagie/text/pdf/SimpleXMLDocHandler.java | 80 -
.../text/pdf/SimpleXMLDocHandlerComment.java | 59 -
.../com/lowagie/text/pdf/SimpleXMLParser.java | 1177 --------
LibrarySource/com/lowagie/text/pdf/SpotColor.java | 84 -
LibrarySource/com/lowagie/text/pdf/TextField.java | 556 ----
.../com/lowagie/text/pdf/TrueTypeFont.java | 1300 ---------
.../com/lowagie/text/pdf/TrueTypeFontSubSet.java | 421 ---
.../com/lowagie/text/pdf/TrueTypeFontUnicode.java | 473 ---
LibrarySource/com/lowagie/text/pdf/Type1Font.java | 808 ------
.../com/lowagie/text/pdf/VerticalText.java | 350 ---
LibrarySource/com/lowagie/text/pdf/XfdfReader.java | 208 --
.../com/lowagie/text/pdf/codec/BmpImage.java | 1307 ---------
.../com/lowagie/text/pdf/codec/CCITTG4Encoder.java | 509 ----
.../com/lowagie/text/pdf/codec/GifImage.java | 592 ----
.../com/lowagie/text/pdf/codec/PngImage.java | 989 -------
.../com/lowagie/text/pdf/codec/TIFFConstants.java | 297 --
.../com/lowagie/text/pdf/codec/TIFFDirectory.java | 657 -----
.../com/lowagie/text/pdf/codec/TIFFFaxDecoder.java | 1480 ----------
.../com/lowagie/text/pdf/codec/TIFFField.java | 472 ---
.../com/lowagie/text/pdf/codec/TIFFLZWDecoder.java | 255 --
.../com/lowagie/text/pdf/codec/TiffImage.java | 477 ---
.../text/pdf/codec/postscript/JavaCharStream.java | 548 ----
.../text/pdf/codec/postscript/MetaDoPS.java | 98 -
.../text/pdf/codec/postscript/PACommand.java | 22 -
.../text/pdf/codec/postscript/PAContext.java | 2053 -------------
.../text/pdf/codec/postscript/PAEngine.java | 144 -
.../text/pdf/codec/postscript/PAParser.java | 305 --
.../pdf/codec/postscript/PAParserConstants.java | 49 -
.../pdf/codec/postscript/PAParserTokenManager.java | 803 -----
.../text/pdf/codec/postscript/PAPencil.java | 401 ---
.../lowagie/text/pdf/codec/postscript/PAToken.java | 70 -
.../pdf/codec/postscript/PainterException.java | 23 -
.../text/pdf/codec/postscript/ParseException.java | 193 --
.../lowagie/text/pdf/codec/postscript/Token.java | 82 -
.../text/pdf/codec/postscript/TokenMgrError.java | 134 -
.../lowagie/text/pdf/codec/postscript/paparser.jj | 290 --
.../com/lowagie/text/pdf/codec/wmf/InputMeta.java | 114 -
.../com/lowagie/text/pdf/codec/wmf/MetaBrush.java | 95 -
.../com/lowagie/text/pdf/codec/wmf/MetaDo.java | 760 -----
.../com/lowagie/text/pdf/codec/wmf/MetaFont.java | 206 --
.../com/lowagie/text/pdf/codec/wmf/MetaObject.java | 72 -
.../com/lowagie/text/pdf/codec/wmf/MetaPen.java | 92 -
.../com/lowagie/text/pdf/codec/wmf/MetaState.java | 367 ---
.../com/lowagie/text/pdf/fonts/Courier-Bold.afm | 343 ---
.../lowagie/text/pdf/fonts/Courier-BoldOblique.afm | 343 ---
.../com/lowagie/text/pdf/fonts/Courier-Oblique.afm | 343 ---
.../com/lowagie/text/pdf/fonts/Courier.afm | 343 ---
.../text/pdf/fonts/FontsResourceAnchor.java | 62 -
.../com/lowagie/text/pdf/fonts/Helvetica-Bold.afm | 2828 ------------------
.../text/pdf/fonts/Helvetica-BoldOblique.afm | 2828 ------------------
.../lowagie/text/pdf/fonts/Helvetica-Oblique.afm | 3052 --------------------
.../com/lowagie/text/pdf/fonts/Helvetica.afm | 3052 --------------------
.../com/lowagie/text/pdf/fonts/Symbol.afm | 214 --
.../com/lowagie/text/pdf/fonts/Times-Bold.afm | 2589 -----------------
.../lowagie/text/pdf/fonts/Times-BoldItalic.afm | 2385 ---------------
.../com/lowagie/text/pdf/fonts/Times-Italic.afm | 2668 -----------------
.../com/lowagie/text/pdf/fonts/Times-Roman.afm | 2420 ----------------
.../com/lowagie/text/pdf/fonts/ZapfDingbats.afm | 226 --
.../lowagie/text/pdf/hyphenation/ByteVector.java | 125 -
.../lowagie/text/pdf/hyphenation/CharVector.java | 135 -
.../com/lowagie/text/pdf/hyphenation/Hyphen.java | 69 -
.../lowagie/text/pdf/hyphenation/Hyphenation.java | 84 -
.../text/pdf/hyphenation/HyphenationException.java | 29 -
.../text/pdf/hyphenation/HyphenationTree.java | 462 ---
.../lowagie/text/pdf/hyphenation/Hyphenator.java | 186 --
.../text/pdf/hyphenation/PatternConsumer.java | 56 -
.../text/pdf/hyphenation/SimplePatternParser.java | 278 --
.../lowagie/text/pdf/hyphenation/TernaryTree.java | 668 -----
LibrarySource/pal/alignment/AbstractAlignment.java | 177 --
LibrarySource/pal/alignment/Alignment.java | 77 -
.../pal/alignment/AlignmentParseException.java | 26 -
LibrarySource/pal/alignment/AlignmentUtils.java | 610 ----
.../pal/alignment/AminoAcidAlignment.java | 102 -
.../pal/alignment/BootstrappedAlignment.java | 75 -
LibrarySource/pal/alignment/CodonAlignment.java | 103 -
.../pal/alignment/ConcatenatedAlignment.java | 89 -
.../pal/alignment/GapBalancedAlignment.java | 230 --
LibrarySource/pal/alignment/JumbledAlignment.java | 78 -
LibrarySource/pal/alignment/ReadAlignment.java | 410 ---
LibrarySource/pal/alignment/SimpleAlignment.java | 181 --
LibrarySource/pal/alignment/SitePattern.java | 253 --
LibrarySource/pal/alignment/StrippedAlignment.java | 213 --
LibrarySource/pal/alignment/makefile | 42 -
LibrarySource/pal/alignment/package.html | 8 -
.../pal/coalescent/CoalescentException.java | 34 -
.../pal/coalescent/CoalescentIntervals.java | 405 ---
.../pal/coalescent/CoalescentSimulator.java | 49 -
LibrarySource/pal/coalescent/CoalescentTree.java | 23 -
LibrarySource/pal/coalescent/ConstExpGrowth.java | 416 ---
.../pal/coalescent/ConstantPopulation.java | 236 --
.../pal/coalescent/DemographicClockTree.java | 110 -
LibrarySource/pal/coalescent/DemographicModel.java | 189 --
LibrarySource/pal/coalescent/DemographicTree.java | 27 -
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.../pal/coalescent/ExponentialGrowth.java | 285 --
.../pal/coalescent/IntervalsExtractor.java | 237 --
LibrarySource/pal/coalescent/SkylinePlot.java | 415 ---
LibrarySource/pal/coalescent/makefile | 42 -
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LibrarySource/pal/datatype/AminoAcids.java | 164 --
LibrarySource/pal/datatype/CodonTable.java | 56 -
LibrarySource/pal/datatype/CodonTableFactory.java | 271 --
LibrarySource/pal/datatype/CodonTableUtils.java | 76 -
LibrarySource/pal/datatype/Codons.java | 73 -
LibrarySource/pal/datatype/DataType.java | 103 -
LibrarySource/pal/datatype/DataTypeUtils.java | 81 -
LibrarySource/pal/datatype/GeneralizedCodons.java | 223 --
LibrarySource/pal/datatype/IUPACNucleotides.java | 148 -
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LibrarySource/pal/datatype/Nucleotides.java | 151 -
LibrarySource/pal/datatype/SimpleDataType.java | 60 -
LibrarySource/pal/datatype/StateRemover.java | 91 -
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.../pal/distance/AlignmentDistanceMatrix.java | 109 -
LibrarySource/pal/distance/DistanceMatrix.java | 286 --
.../pal/distance/DistanceMatrixUtils.java | 121 -
.../pal/distance/DistanceParseException.java | 26 -
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LibrarySource/pal/distance/PairwiseDistance.java | 213 --
LibrarySource/pal/distance/ReadDistanceMatrix.java | 88 -
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LibrarySource/pal/distance/makefile | 42 -
LibrarySource/pal/distance/package.html | 8 -
LibrarySource/pal/eval/ChiSquareValue.java | 196 --
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LibrarySource/pal/eval/LikelihoodValue.java | 1358 ---------
LibrarySource/pal/eval/ModelParameters.java | 236 --
LibrarySource/pal/eval/makefile | 42 -
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LibrarySource/pal/gui/CircularGraphics.java | 213 --
LibrarySource/pal/gui/Painter.java | 26 -
LibrarySource/pal/gui/PositionedNode.java | 80 -
LibrarySource/pal/gui/TreeComponent.java | 152 -
LibrarySource/pal/gui/TreePainter.java | 247 --
LibrarySource/pal/gui/TreePainterCircular.java | 142 -
LibrarySource/pal/gui/TreePainterNormal.java | 168 --
LibrarySource/pal/gui/makefile | 42 -
LibrarySource/pal/gui/package.html | 5 -
LibrarySource/pal/io/FormattedInput.java | 362 ---
LibrarySource/pal/io/FormattedOutput.java | 312 --
LibrarySource/pal/io/InputSource.java | 81 -
LibrarySource/pal/io/OutputTarget.java | 102 -
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LibrarySource/pal/makefile | 52 -
LibrarySource/pal/math/Binomial.java | 81 -
LibrarySource/pal/math/BoundsCheckedFunction.java | 96 -
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LibrarySource/pal/math/DifferentialEvolution.java | 371 ---
LibrarySource/pal/math/ErrorFunction.java | 104 -
LibrarySource/pal/math/GammaFunction.java | 205 --
LibrarySource/pal/math/GeneralizedDEOptimizer.java | 51 -
LibrarySource/pal/math/LineFunction.java | 295 --
LibrarySource/pal/math/MFWithGradient.java | 39 -
LibrarySource/pal/math/MachineAccuracy.java | 45 -
LibrarySource/pal/math/MathUtils.java | 67 -
LibrarySource/pal/math/MersenneTwisterFast.java | 771 -----
LibrarySource/pal/math/MultivariateFunction.java | 54 -
LibrarySource/pal/math/MultivariateMinimum.java | 218 --
LibrarySource/pal/math/NumericalDerivative.java | 138 -
LibrarySource/pal/math/OrthogonalLineFunction.java | 102 -
LibrarySource/pal/math/OrthogonalSearch.java | 80 -
LibrarySource/pal/math/UnivariateFunction.java | 42 -
LibrarySource/pal/math/UnivariateMinimum.java | 479 ---
LibrarySource/pal/math/UrnModel.java | 121 -
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LibrarySource/pal/mep/ConstantMutationRate.java | 198 --
LibrarySource/pal/mep/MutationRateModel.java | 113 -
LibrarySource/pal/mep/SteppedMutationRate.java | 374 ---
LibrarySource/pal/mep/WindowedMutationRate.java | 310 --
LibrarySource/pal/mep/makefile | 42 -
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LibrarySource/pal/misc/BranchLimits.java | 40 -
LibrarySource/pal/misc/GeneralFunction.java | 22 -
LibrarySource/pal/misc/IdGenerator.java | 42 -
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LibrarySource/pal/misc/Identifier.java | 67 -
LibrarySource/pal/misc/Nameable.java | 35 -
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LibrarySource/pal/misc/SimpleSummarizable.java | 56 -
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LibrarySource/pal/misc/TimeOrderCharacterData.java | 387 ---
LibrarySource/pal/misc/TimeStamp.java | 66 -
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LibrarySource/pal/misc/Weighting.java | 26 -
LibrarySource/pal/misc/makefile | 42 -
LibrarySource/pal/misc/package.html | 5 -
.../pal/statistics/BootstrapStatistics.java | 172 --
.../pal/statistics/ChiSquareDistribution.java | 97 -
LibrarySource/pal/statistics/ChiSquareTest.java | 103 -
.../pal/statistics/DiscreteStatistics.java | 234 --
.../pal/statistics/ExponentialDistribution.java | 100 -
.../pal/statistics/GammaDistribution.java | 180 --
.../pal/statistics/KishinoHasegawaTest.java | 202 --
.../pal/statistics/LikelihoodRatioTest.java | 41 -
LibrarySource/pal/statistics/ModelSupport.java | 341 ---
.../pal/statistics/NormalDistribution.java | 99 -
.../pal/statistics/ParetoDistribution.java | 122 -
.../pal/statistics/PenalizedLikelihood.java | 71 -
.../pal/statistics/ShimodairaHasegawaTest.java | 262 --
LibrarySource/pal/statistics/makefile | 42 -
LibrarySource/pal/statistics/package.html | 8 -
.../pal/substmodel/AbstractRateMatrix.java | 278 --
LibrarySource/pal/substmodel/AminoAcidModel.java | 192 --
LibrarySource/pal/substmodel/AminoAcidModelID.java | 36 -
LibrarySource/pal/substmodel/BLOSUM62.java | 195 --
LibrarySource/pal/substmodel/CPREV.java | 210 --
LibrarySource/pal/substmodel/CodonModel.java | 89 -
LibrarySource/pal/substmodel/Dayhoff.java | 198 --
LibrarySource/pal/substmodel/F81.java | 104 -
LibrarySource/pal/substmodel/F84.java | 168 --
LibrarySource/pal/substmodel/GTR.java | 227 --
LibrarySource/pal/substmodel/GammaRates.java | 133 -
LibrarySource/pal/substmodel/HKY.java | 140 -
LibrarySource/pal/substmodel/InvariableSites.java | 126 -
LibrarySource/pal/substmodel/JTT.java | 197 --
LibrarySource/pal/substmodel/MTREV24.java | 196 --
.../pal/substmodel/MatrixExponential.java | 894 ------
LibrarySource/pal/substmodel/NucleotideModel.java | 132 -
.../pal/substmodel/NucleotideModelID.java | 34 -
LibrarySource/pal/substmodel/RateDistribution.java | 92 -
LibrarySource/pal/substmodel/RateMatrix.java | 86 -
LibrarySource/pal/substmodel/RateMatrixUtils.java | 64 -
.../pal/substmodel/SubstitutionModel.java | 288 --
LibrarySource/pal/substmodel/TN.java | 183 --
.../pal/substmodel/TransitionProbability.java | 48 -
LibrarySource/pal/substmodel/TwoStateModel.java | 115 -
LibrarySource/pal/substmodel/UniformRate.java | 84 -
LibrarySource/pal/substmodel/VT.java | 210 --
LibrarySource/pal/substmodel/WAG.java | 210 --
LibrarySource/pal/substmodel/YangCodonModel.java | 276 --
LibrarySource/pal/substmodel/makefile | 42 -
LibrarySource/pal/substmodel/package.html | 9 -
LibrarySource/pal/tree/ClockTree.java | 143 -
LibrarySource/pal/tree/DatedTipsClockTree.java | 446 ---
LibrarySource/pal/tree/LogParameterizedTree.java | 100 -
LibrarySource/pal/tree/MutationRateModelTree.java | 175 --
LibrarySource/pal/tree/NeighborJoiningTree.java | 209 --
LibrarySource/pal/tree/Node.java | 138 -
LibrarySource/pal/tree/NodeFactory.java | 40 -
LibrarySource/pal/tree/NodeUtils.java | 629 ----
LibrarySource/pal/tree/ParameterizedTree.java | 112 -
LibrarySource/pal/tree/ReadTree.java | 157 -
LibrarySource/pal/tree/SUPGMATree.java | 102 -
LibrarySource/pal/tree/SimpleNode.java | 448 ---
LibrarySource/pal/tree/SimpleTree.java | 274 --
LibrarySource/pal/tree/SimulatedAlignment.java | 211 --
LibrarySource/pal/tree/SplitSystem.java | 127 -
LibrarySource/pal/tree/SplitUtils.java | 169 --
LibrarySource/pal/tree/Tree.java | 72 -
LibrarySource/pal/tree/TreeDistanceMatrix.java | 135 -
LibrarySource/pal/tree/TreeParseException.java | 26 -
LibrarySource/pal/tree/TreeUtils.java | 1042 -------
LibrarySource/pal/tree/UPGMATree.java | 201 --
LibrarySource/pal/tree/UnconstrainedTree.java | 110 -
LibrarySource/pal/tree/makefile | 42 -
LibrarySource/pal/tree/package.html | 8 -
LibrarySource/pal/util/Comparable.java | 36 -
LibrarySource/pal/util/ComparableDouble.java | 50 -
LibrarySource/pal/util/Comparator.java | 37 -
LibrarySource/pal/util/HeapSort.java | 411 ---
LibrarySource/pal/util/Log.java | 55 -
LibrarySource/pal/util/Logger.java | 25 -
LibrarySource/pal/util/ThreeNumberSort.java | 237 --
LibrarySource/pal/util/makefile | 42 -
LibrarySource/pal/util/package.html | 5 -
465 files changed, 154598 deletions(-)
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