X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=bf1481a28a24a0bebd6610351749e8ae0910892f;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=bb90d2df0193e6d0fc598bed45b3da3d83a9aaec;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index bb90d2d..bf1481a 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,14 +20,18 @@ */ package jalview.io; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; import java.io.IOException; +import java.util.ArrayList; import java.util.Enumeration; import java.util.Hashtable; +import java.util.List; import java.util.Vector; /** @@ -50,7 +54,12 @@ public abstract class AlignFile extends FileParse /** * annotation to be added to generated alignment object */ - protected Vector annotations; + protected Vector annotations; + + /** + * SequenceGroups to be added to the alignment object + */ + protected List seqGroups; /** * Properties to be added to generated alignment object @@ -63,13 +72,17 @@ public abstract class AlignFile extends FileParse boolean jvSuffix = true; + private boolean parseCalled; + /** * Creates a new AlignFile object. */ public AlignFile() { - // Shouldn't we init data structures (JBPNote: not sure - initData is for initialising the structures used for reading from a datasource, and the bare constructor hasn't got any datasource) - initData(); + // Shouldn't we init data structures (JBPNote: not sure - initData is for + // initialising the structures used for reading from a datasource, and the + // bare constructor hasn't got any datasource) + initData(); } /** @@ -82,13 +95,29 @@ public abstract class AlignFile extends FileParse */ public AlignFile(String inFile, String type) throws IOException { + this(true, inFile, type); + } + + /** + * Constructor which (optionally delays) parsing of data from a file of some + * specified type. + * + * @param parseImmediately + * if false, need to call 'doParse()' to begin parsing data + * @param inFile + * Filename to read from. + * @param type + * What type of file to read from (File, URL) + * @throws IOException + */ + public AlignFile(boolean parseImmediately, String inFile, String type) + throws IOException + { super(inFile, type); initData(); - parse(); - // sets the index of each sequence in the alignment - for (int i = 0, c = seqs.size(); i < c; i++) + if (parseImmediately) { - seqs.get(i).setIndex(i); + doParse(); } } @@ -101,8 +130,42 @@ public abstract class AlignFile extends FileParse */ public AlignFile(FileParse source) throws IOException { + this(true, source); + } + + /** + * Construct a new parser to read from the position where some other parsing + * process left + * + * @param parseImmediately + * if false, need to call 'doParse()' to begin parsing data + * @param source + */ + public AlignFile(boolean parseImmediately, FileParse source) + throws IOException + { super(source); initData(); + if (parseImmediately) + { + doParse(); + } + } + + /** + * called if parsing was delayed till after parser was constructed + * + * @throws IOException + */ + public void doParse() throws IOException + { + if (parseCalled) + { + throw new IOException( + "Implementation error: Parser called twice for same data.\n" + + "Need to call initData() again before parsing can be reattempted."); + } + parseCalled = true; parse(); // sets the index of each sequence in the alignment for (int i = 0, c = seqs.size(); i < c; i++) @@ -119,6 +182,11 @@ public abstract class AlignFile extends FileParse return seqs; } + public List getSeqGroups() + { + return seqGroups; + } + /** * Return the Sequences in the seqs Vector as an array of Sequences */ @@ -128,7 +196,7 @@ public abstract class AlignFile extends FileParse for (int i = 0; i < seqs.size(); i++) { - s[i] = (SequenceI) seqs.elementAt(i); + s[i] = seqs.elementAt(i); } return s; @@ -140,7 +208,7 @@ public abstract class AlignFile extends FileParse * * @param al */ - public void addAnnotations(Alignment al) + public void addAnnotations(AlignmentI al) { addProperties(al); for (int i = 0; i < annotations.size(); i++) @@ -152,8 +220,7 @@ public abstract class AlignFile extends FileParse * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i)); * Rna.HelixMap(pairArray); */ - AlignmentAnnotation an = (AlignmentAnnotation) annotations - .elementAt(i); + AlignmentAnnotation an = annotations.elementAt(i); an.validateRangeAndDisplay(); al.addAnnotation(an); } @@ -161,13 +228,24 @@ public abstract class AlignFile extends FileParse } /** + * register sequence groups on the alignment for **output** + * + * @param al + */ + public void addSeqGroups(AlignmentI al) + { + this.seqGroups = al.getGroups(); + + } + + /** * Add any additional information extracted from the file to the alignment * properties. * * @note implicitly called by addAnnotations() * @param al */ - public void addProperties(Alignment al) + public void addProperties(AlignmentI al) { if (properties != null && properties.size() > 0) { @@ -195,7 +273,8 @@ public abstract class AlignFile extends FileParse if (key == null) { throw new Error( - "Implementation error: Cannot have null alignment property key."); + MessageManager + .getString("error.implementation_error_cannot_have_null_alignment")); } if (value == null) { @@ -222,8 +301,10 @@ public abstract class AlignFile extends FileParse */ protected void initData() { - seqs = new Vector(); - annotations = new Vector(); + seqs = new Vector(); + annotations = new Vector(); + seqGroups = new ArrayList(); + parseCalled = false; } /** @@ -234,7 +315,7 @@ public abstract class AlignFile extends FileParse */ protected void setSeqs(SequenceI[] s) { - seqs = new Vector(); + seqs = new Vector(); for (int i = 0; i < s.length; i++) { @@ -294,25 +375,29 @@ public abstract class AlignFile extends FileParse /** * vector of String[] treeName, newickString pairs */ - Vector newickStrings = null; + Vector newickStrings = null; protected void addNewickTree(String treeName, String newickString) { if (newickStrings == null) { - newickStrings = new Vector(); + newickStrings = new Vector(); } - newickStrings.addElement(new String[] - { treeName, newickString }); + newickStrings.addElement(new String[] { treeName, newickString }); } protected int getTreeCount() { - if (newickStrings == null) + return newickStrings == null ? 0 : newickStrings.size(); + } + + public void addGroups(AlignmentI al) + { + + for (SequenceGroup sg : getSeqGroups()) { - return 0; + al.addGroup(sg); } - return newickStrings.size(); } }