From: Mark G. <mg...@us...> - 2003-04-03 01:11:39
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Update of /cvsroot/gmod/apollo/src/java/apollo/gui/menus In directory sc8-pr-cvs1:/tmp/cvs-serv28038/src/java/apollo/gui/menus Modified Files: TierPopupMenu.java Log Message: Worked on getting game features to come up in blixem. More features are now coming up but not all of them. Not sure why. The issue I dealt with was that most FeaturePair hits do not have ref sequences with residues. Its actually not in the xml. The workaround that is also employed in DrawableResultSeqFeature is to get the alignment sequence which is the properties hash as "subject_alignment". This is something that needs to be cleaned up in game. Perhaps a getHitAlignmentSequence in FeaturePair as well as maybe stuffing the alignment seq in as the ref seq if the subject sequence is absent as is often the case. Is blixem written in java? It runs as an executable from the command line. I think ideally we would want an alignment viewer in java so they can easily interact (follow selection, highlight bars for region...) Index: TierPopupMenu.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/menus/TierPopupMenu.java,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** TierPopupMenu.java 1 Apr 2003 01:50:25 -0000 1.23 --- TierPopupMenu.java 3 Apr 2003 01:11:35 -0000 1.24 *************** *** 549,553 **** return tier_labels; } ! public Vector findTypes() { Vector types = new Vector(); --- 549,555 ---- return tier_labels; } ! ! /** Returns a vector with a unique list of all types being used in ! selection in view. */ public Vector findTypes() { Vector types = new Vector(); *************** *** 555,558 **** --- 557,561 ---- FeatureView fv = (FeatureView)view; + // this needs to be changed to getSelectionDescendedFromModel Vector f = ap.getSelection().getSelectedData(fv); |