X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=497f0a580836af85016458f6f32c3ecd97adc9a3;hb=6fd29e7e2753c9066fa31b76ab71827f96d471ff;hp=e4891f08281178db8b9a1c5536cb3099c8d07626;hpb=ebe0c31476d408f10e968bed024e898c02c7204e;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index e4891f0..497f0a5 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -20,7 +20,6 @@ */ package jalview.io; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; @@ -42,13 +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; @@ -65,15 +66,26 @@ public abstract class AlignFile extends FileParse /** * Properties to be added to generated alignment object */ - protected Hashtable properties; + private Hashtable properties; long start; long end; - boolean jvSuffix = true; + /** + * true if parse() has been called + */ + private boolean parseCalled = false; - private boolean parseCalled; + private boolean parseImmediately = true; + + /** + * @return if doParse() was called at construction time + */ + protected boolean isParseImmediately() + { + return parseImmediately; + } /** * Creates a new AlignFile object. @@ -86,38 +98,49 @@ 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. @@ -127,25 +150,36 @@ 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) { + + // stash flag in case parse needs to know if it has to autoconfigure or was + // configured after construction + this.parseImmediately = parseImmediately; + + if (parseImmediately) + { doParse(); } } + /** * called if parsing was delayed till after parser was constructed + * * @throws IOException */ public void doParse() throws IOException @@ -156,16 +190,10 @@ 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 */ @@ -182,6 +210,7 @@ public abstract class AlignFile extends FileParse /** * Return the Sequences in the seqs Vector as an array of Sequences */ + @Override public SequenceI[] getSeqsAsArray() { SequenceI[] s = new SequenceI[seqs.size()]; @@ -200,7 +229,8 @@ 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++) @@ -212,14 +242,18 @@ public abstract class AlignFile extends FileParse * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i)); * Rna.HelixMap(pairArray); */ - AlignmentAnnotation an = annotations - .elementAt(i); + AlignmentAnnotation an = annotations.elementAt(i); an.validateRangeAndDisplay(); al.addAnnotation(an); } } + /** + * register sequence groups on the alignment for **output** + * + * @param al + */ public void addSeqGroups(AlignmentI al) { this.seqGroups = al.getGroups(); @@ -233,7 +267,7 @@ public abstract class AlignFile extends FileParse * @note implicitly called by addAnnotations() * @param al */ - public void addProperties(Alignment al) + public void addProperties(AlignmentI al) { if (properties != null && properties.size() > 0) { @@ -260,7 +294,8 @@ 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) { @@ -290,7 +325,7 @@ public abstract class AlignFile extends FileParse seqs = new Vector(); annotations = new Vector(); seqGroups = new ArrayList(); - parseCalled=false; + parseCalled = false; } /** @@ -299,7 +334,8 @@ public abstract class AlignFile extends FileParse * @param s * DOCUMENT ME! */ - protected void setSeqs(SequenceI[] s) + @Override + public void setSeqs(SequenceI[] s) { seqs = new Vector(); @@ -315,16 +351,6 @@ 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 @@ -337,7 +363,15 @@ 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 { @@ -348,14 +382,21 @@ 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); } /** @@ -369,8 +410,7 @@ public abstract class AlignFile extends FileParse { newickStrings = new Vector(); } - newickStrings.addElement(new String[] - { treeName, newickString }); + newickStrings.addElement(new String[] { treeName, newickString }); } protected int getTreeCount() @@ -378,6 +418,7 @@ public abstract class AlignFile extends FileParse return newickStrings == null ? 0 : newickStrings.size(); } + @Override public void addGroups(AlignmentI al) { @@ -387,4 +428,8 @@ public abstract class AlignFile extends FileParse } } + protected void addSequence(SequenceI seq) + { + seqs.add(seq); + } }