From: Suzanna L. <su...@us...> - 2002-03-03 05:55:48
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Update of /cvsroot/gmod/apollo/src/java/apollo/datamodel In directory usw-pr-cvs1:/tmp/cvs-serv2523/apollo/datamodel Modified Files: FeatureSet.java Gene.java SeqFeature.java Log Message: found the bug for moving things to opposite strand. it comes about from the unnatural split (again this causes complexities) of the forward and reverse strands. need to keep track of the two separate feature sets as a unit in the adapter so that this can be solved. ugh. Index: FeatureSet.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/FeatureSet.java,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -d -r1.44 -r1.45 *** FeatureSet.java 1 Mar 2002 23:50:08 -0000 1.44 --- FeatureSet.java 3 Mar 2002 05:55:45 -0000 1.45 *************** *** 41,68 **** } ! if (!features.contains (feature)) ! { ! features.addElement(feature); ! feature.setRefFeature (this); ! ! if (features.size() == 1) ! { ! /* first time through, just use them */ ! setStart (feature.getStart()); ! setEnd (feature.getEnd()); ! } ! else ! { ! /* this does assume that all of the spans are in the same ! direction - issue a warning if not? */ ! /* something that is one base long doesn't have a ! direction, but its okay to add in any case */ ! adjustEdges (feature); ! } ! // Set the reference sequence here ! if (getRefSequence() != null) { ! feature.setRefSequence(getRefSequence()); ! } } } --- 41,67 ---- } ! if (!features.contains (feature)) { ! features.addElement(feature); ! feature.setRefFeature (this); ! ! if (features.size() == 1) ! { ! /* first time through, just use them */ ! setStart (feature.getStart()); ! setEnd (feature.getEnd()); ! } ! else ! { ! /* this does assume that all of the spans are in the same ! direction - issue a warning if not? */ ! /* something that is one base long doesn't have a ! direction, but its okay to add in any case */ ! adjustEdges (feature); ! } ! // Set the reference sequence here ! if (getRefSequence() != null) { ! feature.setRefSequence(getRefSequence()); ! } } } Index: Gene.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/Gene.java,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -d -r1.36 -r1.37 *** Gene.java 25 Jan 2002 23:43:57 -0000 1.36 --- Gene.java 3 Mar 2002 05:55:45 -0000 1.37 *************** *** 102,131 **** } - /* - // only update the name of transcripts and genes that follow the - // automatic naming convention - */ - public void setName(String name) { - /* Don't hide this, - make the application do set transcript names explicitly - String old_name = this.getName(); - for (int i=0; i < getTranscripts().size(); i++) { - Transcript t = (Transcript) getTranscripts().elementAt(i); - String t_name = t.getName(); - if (t_name == null || - t_name.indexOf (old_name) >= 0) - { - String t_suffix = ((t_name == null || - t_name.indexOf (":") < 0) ? - ":" + (i+1) : - t_name.substring (t_name.indexOf (":"))); - t.setName(name + t_suffix); - System.err.println("reset transcript name to " + t.getName()); - } - } - */ - super.setName(name); - } - public static void main(String[] args) { Transcript tran1 = new Transcript(); --- 102,105 ---- Index: SeqFeature.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/datamodel/SeqFeature.java,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -d -r1.44 -r1.45 *** SeqFeature.java 17 Feb 2002 07:21:09 -0000 1.44 --- SeqFeature.java 3 Mar 2002 05:55:45 -0000 1.45 *************** *** 113,117 **** public void setHigh(long high) { ! this.high = high; } --- 113,117 ---- public void setHigh(long high) { ! this.high = high; } *************** *** 258,264 **** if (name == null) { throw new NullPointerException("Can't accept feature name of null. " + ! "Use SeqFeatureI.NO_NAME or 'SeqFeatureI.NO_NAME' instead."); } ! this.name = name; } --- 258,265 ---- if (name == null) { throw new NullPointerException("Can't accept feature name of null. " + ! "Use SeqFeatureI.NO_NAME instead."); } ! else ! this.name = name; } |