X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=5760fbe385781550f72b6bace208a6f9da3f2ab5;hb=894672b99c68bc0562ef5a3a0396a4825c8d7d48;hp=5d8a29784e718d4f80c76e29d77a71f5f68cecfd;hpb=b8f13fd9ac44853d6510eac85edb60b117dc4620;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 5d8a297..5760fbe 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -20,14 +20,6 @@ */ package jalview.io; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Vector; - -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; @@ -35,6 +27,13 @@ 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; + /** * DOCUMENT ME! * @@ -48,7 +47,8 @@ public abstract class AlignFile extends FileParse 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; @@ -89,35 +89,39 @@ public abstract class AlignFile extends FileParse /** * Constructor which parses the data from a file of some specified type. * - * @param inFile - * Filename to read from. + * @param dataObject + * Filename, URL or Pasted String to read from. * @param type - * What type of file to read from (File, URL) + * What type of file to read from (File, URL, Pasted String) */ - public AlignFile(String inFile, String type) throws IOException + public AlignFile(String dataObject, String type) throws IOException { - this(true, inFile, type); + this(true, dataObject, type); } - + /** - * 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 dataObject + * Filename, URL or Pasted String 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 + public AlignFile(boolean parseImmediately, String dataObject, String type) + throws IOException { - super(inFile, type); + super(dataObject, type); initData(); - if (parseImmediately) { + if (parseImmediately) + { doParse(); } } + /** * Attempt to read from the position where some other parsing process left * off. @@ -127,25 +131,31 @@ 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 @@ -156,7 +166,7 @@ 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++) @@ -165,7 +175,6 @@ public abstract class AlignFile extends FileParse } } - /** * Return the seqs Vector */ @@ -200,7 +209,7 @@ 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++) @@ -212,14 +221,18 @@ 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 +246,7 @@ 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 +273,9 @@ 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 +305,7 @@ public abstract class AlignFile extends FileParse seqs = new Vector(); annotations = new Vector(); seqGroups = new ArrayList(); - parseCalled=false; + parseCalled = false; } /** @@ -337,7 +352,15 @@ 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 { @@ -369,8 +392,7 @@ public abstract class AlignFile extends FileParse { newickStrings = new Vector(); } - newickStrings.addElement(new String[] - { treeName, newickString }); + newickStrings.addElement(new String[] { treeName, newickString }); } protected int getTreeCount() @@ -378,4 +400,13 @@ public abstract class AlignFile extends FileParse return newickStrings == null ? 0 : newickStrings.size(); } + public void addGroups(AlignmentI al) + { + + for (SequenceGroup sg : getSeqGroups()) + { + al.addGroup(sg); + } + } + }