X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=c931cb837f62e737cbd5b4090b1649839bab1002;hb=9289ad58228571a63fdf54ef720603a590d58adc;hp=661ebae135ec184b8b2f1c35b2a73693d55f6de1;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 661ebae..c931cb8 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 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,15 +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; /** @@ -38,13 +41,15 @@ import java.util.Vector; * @version $Revision$ */ public abstract class AlignFile extends FileParse + implements AlignmentFileReaderI, AlignmentFileWriterI { int noSeqs = 0; int maxLength = 0; /** - * Sequences to be added to form a new alignment. + * Sequences to be added to form a new alignment. TODO: remove vector in this + * class */ protected Vector seqs; @@ -54,16 +59,19 @@ public abstract class AlignFile extends FileParse protected Vector annotations; /** + * SequenceGroups to be added to the alignment object + */ + protected List seqGroups; + + /** * Properties to be added to generated alignment object */ - protected Hashtable properties; + private Hashtable properties; long start; long end; - boolean jvSuffix = true; - private boolean parseCalled; /** @@ -77,38 +85,49 @@ public abstract class AlignFile extends FileParse initData(); } + public AlignFile(SequenceI[] seqs) + { + this(); + setSeqs(seqs); + } + /** * Constructor which parses the data from a file of some specified type. * - * @param inFile - * Filename to read from. - * @param type - * What type of file to read from (File, URL) + * @param dataObject + * Filename, URL or Pasted String to read from. + * @param sourceType + * What type of file to read from (File, URL, Pasted String) */ - public AlignFile(String inFile, String type) throws IOException + public AlignFile(String dataObject, DataSourceType sourceType) + throws IOException { - this(true, inFile, type); + this(true, dataObject, sourceType); } - + /** - * Constructor which (optionally delays) parsing of data from a file of some specified 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 + * @param dataObject + * Filename, URL or Pasted String to read from. + * @param sourceType * What type of file to read from (File, URL) * @throws IOException */ - public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException + public AlignFile(boolean parseImmediately, String dataObject, + DataSourceType sourceType) throws IOException { - super(inFile, type); + super(dataObject, sourceType); initData(); - if (parseImmediately) { + if (parseImmediately) + { doParse(); } } + /** * Attempt to read from the position where some other parsing process left * off. @@ -118,25 +137,31 @@ public abstract class AlignFile extends FileParse */ public AlignFile(FileParse source) throws IOException { - this(true,source); + this(true, source); } + /** - * Construct a new parser to read from the position where some other parsing process left + * 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 + public AlignFile(boolean parseImmediately, FileParse source) + throws IOException { super(source); initData(); - if (parseImmediately) { + if (parseImmediately) + { doParse(); } } + /** * called if parsing was delayed till after parser was constructed + * * @throws IOException */ public void doParse() throws IOException @@ -147,16 +172,10 @@ public abstract class AlignFile extends FileParse "Implementation error: Parser called twice for same data.\n" + "Need to call initData() again before parsing can be reattempted."); } - parseCalled=true; + parseCalled = true; parse(); - // sets the index of each sequence in the alignment - for (int i = 0, c = seqs.size(); i < c; i++) - { - seqs.get(i).setIndex(i); - } } - /** * Return the seqs Vector */ @@ -165,16 +184,22 @@ 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 */ + @Override public SequenceI[] getSeqsAsArray() { SequenceI[] s = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { - s[i] = (SequenceI) seqs.elementAt(i); + s[i] = seqs.elementAt(i); } return s; @@ -186,7 +211,8 @@ public abstract class AlignFile extends FileParse * * @param al */ - public void addAnnotations(Alignment al) + @Override + public void addAnnotations(AlignmentI al) { addProperties(al); for (int i = 0; i < annotations.size(); i++) @@ -198,8 +224,7 @@ 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); } @@ -207,13 +232,24 @@ 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) { @@ -240,7 +276,8 @@ public abstract class AlignFile extends FileParse { if (key == null) { - throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_have_null_alignment")); } if (value == null) { @@ -267,9 +304,10 @@ public abstract class AlignFile extends FileParse */ protected void initData() { - seqs = new Vector(); - annotations = new Vector(); - parseCalled=false; + seqs = new Vector<>(); + annotations = new Vector<>(); + seqGroups = new ArrayList<>(); + parseCalled = false; } /** @@ -278,9 +316,10 @@ public abstract class AlignFile extends FileParse * @param s * DOCUMENT ME! */ - protected void setSeqs(SequenceI[] s) + @Override + public void setSeqs(SequenceI[] s) { - seqs = new Vector(); + seqs = new Vector<>(); for (int i = 0; i < s.length; i++) { @@ -294,16 +333,6 @@ public abstract class AlignFile extends FileParse public abstract void parse() throws IOException; /** - * Print out in alignment file format the Sequences in the seqs Vector. - */ - public abstract String print(); - - public void addJVSuffix(boolean b) - { - jvSuffix = b; - } - - /** * A general parser for ids. * * @String id Id to be parsed @@ -316,7 +345,15 @@ public abstract class AlignFile extends FileParse if (space > -1) { seq = new Sequence(id.substring(0, space), ""); - seq.setDescription(id.substring(space + 1)); + String desc = id.substring(space + 1); + seq.setDescription(desc); + + /* + * it is tempting to parse Ensembl style gene description e.g. + * chromosome:GRCh38:7:140696688:140721955:1 and set the + * start position of the sequence, but this causes much confusion + * for reverse strand feature locations + */ } else { @@ -327,38 +364,63 @@ public abstract class AlignFile extends FileParse } /** - * Creates the output id. Adds prefix Uniprot format source|id And suffix - * Jalview /start-end + * Creates the output id. Adds prefix Uniprot format source|id and optionally + * suffix Jalview /start-end + * + * @param jvsuffix * * @String id Id to be parsed */ + String printId(SequenceI seq, boolean jvsuffix) + { + return seq.getDisplayId(jvsuffix); + } + String printId(SequenceI seq) { - return seq.getDisplayId(jvSuffix); + return printId(seq, true); } /** * 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(); + } + + @Override + public void addGroups(AlignmentI al) + { + + for (SequenceGroup sg : getSeqGroups()) { - return 0; + al.addGroup(sg); } - return newickStrings.size(); + } + + protected void addSequence(SequenceI seq) + { + seqs.add(seq); + } + + @Override + public Object[] preprocess() + { + // most AlignFiles will not need to return any preprocessing information + // those that do should override this method + return null; } }