From 4994a7487ffa3ac5378520051f8e317a7954b204 Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Thu, 4 Jan 2018 20:17:49 +0000 Subject: [PATCH] JAL-281 ForesterParser factory methods added --- src/jalview/ext/forester/io/ForesterParser.java | 88 +++++++++++++++++++++- src/jalview/ext/forester/io/ForesterReader.java | 91 ----------------------- src/jalview/ext/forester/io/NexusParser.java | 87 ---------------------- src/jalview/ext/forester/io/PhyloXMLParser.java | 86 --------------------- src/jalview/io/FileFormat.java | 10 +-- 5 files changed, 89 insertions(+), 273 deletions(-) delete mode 100644 src/jalview/ext/forester/io/ForesterReader.java delete mode 100644 src/jalview/ext/forester/io/NexusParser.java delete mode 100644 src/jalview/ext/forester/io/PhyloXMLParser.java diff --git a/src/jalview/ext/forester/io/ForesterParser.java b/src/jalview/ext/forester/io/ForesterParser.java index 1167e13..851b12b 100644 --- a/src/jalview/ext/forester/io/ForesterParser.java +++ b/src/jalview/ext/forester/io/ForesterParser.java @@ -1,22 +1,27 @@ package jalview.ext.forester.io; +import jalview.api.FeatureSettingsModelI; +import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.ext.archaeopteryx.Tree; import jalview.ext.treeviewer.TreeI; import jalview.ext.treeviewer.TreeParserI; +import jalview.io.AlignmentFileReaderI; +import jalview.io.DataSourceType; +import jalview.io.FileParse; import java.io.IOException; import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.phylogeny.Phylogeny; -public class ForesterParser implements TreeParserI +public class ForesterParser implements TreeParserI, AlignmentFileReaderI { private final PhylogenyParser parser; - private SequenceI[] seqs; - - public ForesterParser(PhylogenyParser foresterParser) + protected ForesterParser(PhylogenyParser foresterParser, FileParse source) { parser = foresterParser; } @@ -47,4 +52,79 @@ public class ForesterParser implements TreeParserI { return parser.getName(); } + + @Override + public SequenceI[] getSeqsAsArray() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public void addAnnotations(AlignmentI al) + { + // TODO Auto-generated method stub + + } + + @Override + public void addGroups(AlignmentI al) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSeqs(SequenceI[] sequencesArray) + { + // TODO Auto-generated method stub + + } + + @Override + public boolean hasWarningMessage() + { + // TODO Auto-generated method stub + return false; + } + + @Override + public String getWarningMessage() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public String getInFile() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public DataSourceType getDataSourceType() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public FeatureSettingsModelI getFeatureColourScheme() + { + // TODO Auto-generated method stub + return null; + } + + public static ForesterParser createNexusParser(FileParse source) + { + return new ForesterParser(new NexusPhylogeniesParser(), source); + } + + public static ForesterParser createPhyloXmlParser(FileParse source) + { + // support non-xsd validating? + return new ForesterParser( + PhyloXmlParser.createPhyloXmlParserXsdValidating(), source); + } } \ No newline at end of file diff --git a/src/jalview/ext/forester/io/ForesterReader.java b/src/jalview/ext/forester/io/ForesterReader.java deleted file mode 100644 index 625a151..0000000 --- a/src/jalview/ext/forester/io/ForesterReader.java +++ /dev/null @@ -1,91 +0,0 @@ -package jalview.ext.forester.io; - -import jalview.api.FeatureSettingsModelI; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceI; -import jalview.io.AlignmentFileReaderI; -import jalview.io.DataSourceType; -import jalview.io.FileParse; - -public class ForesterReader implements AlignmentFileReaderI -{ - - public ForesterReader(FileParse source) - { - // if (source.getDataSourceType() == DataSourceType.URL) - // { - // ParserUtils.createParserDependingOnUrlContents(url, - // AptxInit.APTX_CONFIG.isValidatePhyloXmlAgainstSchema()); - // - // } - // else - // { - // ParserUtils.createParserDependingOnFileType(file, - // AptxInit.APTX_CONFIG.isValidatePhyloXmlAgainstSchema()); - // } - } - - @Override - public SequenceI[] getSeqsAsArray() - { - // TODO Auto-generated method stub - return null; - } - - @Override - public void addAnnotations(AlignmentI al) - { - // TODO Auto-generated method stub - - } - - @Override - public void addGroups(AlignmentI al) - { - // TODO Auto-generated method stub - - } - - @Override - public void setSeqs(SequenceI[] sequencesArray) - { - // TODO Auto-generated method stub - - } - - @Override - public boolean hasWarningMessage() - { - // TODO Auto-generated method stub - return false; - } - - @Override - public String getWarningMessage() - { - // TODO Auto-generated method stub - return null; - } - - @Override - public String getInFile() - { - // TODO Auto-generated method stub - return null; - } - - @Override - public DataSourceType getDataSourceType() - { - // TODO Auto-generated method stub - return null; - } - - @Override - public FeatureSettingsModelI getFeatureColourScheme() - { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/src/jalview/ext/forester/io/NexusParser.java b/src/jalview/ext/forester/io/NexusParser.java deleted file mode 100644 index f15c6f2..0000000 --- a/src/jalview/ext/forester/io/NexusParser.java +++ /dev/null @@ -1,87 +0,0 @@ -// package jalview.ext.forester.io; -// -// import jalview.api.FeatureSettingsModelI; -// import jalview.datamodel.AlignmentI; -// import jalview.datamodel.SequenceI; -// import jalview.io.AlignmentFileReaderI; -// import jalview.io.DataSourceType; -// -// import org.forester.io.parsers.nexus.NexusPhylogeniesParser; -// -// public class NexusParser extends ForesterParser -// implements AlignmentFileReaderI -// { -// NexusPhylogeniesParser nxParser; -// -// public NexusParser() -// { -// nxParser = new NexusPhylogeniesParser(); -// -// } -// -// @Override -// public SequenceI[] getSeqsAsArray() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public void addAnnotations(AlignmentI al) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public void addGroups(AlignmentI al) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public void setSeqs(SequenceI[] sequencesArray) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public boolean hasWarningMessage() -// { -// // TODO Auto-generated method stub -// return false; -// } -// -// @Override -// public String getWarningMessage() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public String getInFile() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public DataSourceType getDataSourceType() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public FeatureSettingsModelI getFeatureColourScheme() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// -// -// } \ No newline at end of file diff --git a/src/jalview/ext/forester/io/PhyloXMLParser.java b/src/jalview/ext/forester/io/PhyloXMLParser.java deleted file mode 100644 index e877d41..0000000 --- a/src/jalview/ext/forester/io/PhyloXMLParser.java +++ /dev/null @@ -1,86 +0,0 @@ -// package jalview.ext.forester.io; -// -// import jalview.api.FeatureSettingsModelI; -// import jalview.datamodel.AlignmentI; -// import jalview.datamodel.SequenceI; -// import jalview.io.AlignmentFileReaderI; -// import jalview.io.DataSourceType; -// -// import org.forester.io.parsers.PhylogenyParser; -// import org.forester.io.parsers.phyloxml.PhyloXmlParser; -// -// public class PhyloXMLParser extends ForesterParser -// implements AlignmentFileReaderI -// { -// PhyloXmlParser phxmlParser = PhyloXmlParser -// .createPhyloXmlParserXsdValidating(); -// -// public PhyloXMLParser(PhylogenyParser foresterParser) -// { -// super(foresterParser); -// } -// -// @Override -// public SequenceI[] getSeqsAsArray() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public void addAnnotations(AlignmentI al) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public void addGroups(AlignmentI al) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public void setSeqs(SequenceI[] sequencesArray) -// { -// // TODO Auto-generated method stub -// -// } -// -// @Override -// public boolean hasWarningMessage() -// { -// // TODO Auto-generated method stub -// return false; -// } -// -// @Override -// public String getWarningMessage() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public String getInFile() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public DataSourceType getDataSourceType() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// @Override -// public FeatureSettingsModelI getFeatureColourScheme() -// { -// // TODO Auto-generated method stub -// return null; -// } -// -// } \ No newline at end of file diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java index ef4a2be..e737c35 100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@ -22,7 +22,7 @@ package jalview.io; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; -import jalview.ext.forester.io.ForesterReader; +import jalview.ext.forester.io.ForesterParser; import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; @@ -382,13 +382,13 @@ public enum FileFormat implements FileFormatI public AlignmentFileReaderI getReader(FileParse source) throws IOException { - return new ForesterReader(source); + return ForesterParser.createNexusParser(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { - // TODO Auto-generated method stub + // handle within Aptx? return null; } @@ -406,13 +406,13 @@ public enum FileFormat implements FileFormatI public AlignmentFileReaderI getReader(FileParse source) throws IOException { - return new ForesterReader(source); + return ForesterParser.createPhyloXmlParser(source); } @Override public AlignmentFileWriterI getWriter(AlignmentI al) { - // TODO Auto-generated method stub + // handle within Aptx? return null; } -- 1.7.10.2