From: Suzanna L. <su...@us...> - 2003-11-30 04:58:54
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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism In directory sc8-pr-cvs1:/tmp/cvs-serv6686/apollo/dataadapter/organism Modified Files: DefaultNameAdapter.java Log Message: well, this is a big commit. waited a long time to proceed with it. 1. holder no longer exists as an inherent aspect of seqfeatures. this is all handled now within the gui drawables. each drawable has a couple attributes that determine when to draw the feature it is associated with. one is the draw-level. this indicates the depth of the feature hierarchy that the drawable can represent. e.g. a draw_level of 2 means it can draw a seqfeature and its direct parent and a draw_level of 1 means it can only represent the seqfeature itself. 2. drawables no longer implement the datamodel interfaces. they are truly just drawables/glyphs that can represent the model. 3. added 2 more analysis parsers for repeatmasker and trnascan 4. added some gui utilities to reduce duplicated code 5. changed the format of the tiers files to be tag : value. the code will still read the old format, but will automatically update it to the new format. hmmm, think that is it. still doing more testing, but so far so good Index: DefaultNameAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/DefaultNameAdapter.java,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** DefaultNameAdapter.java 13 Nov 2003 11:30:10 -0000 1.9 --- DefaultNameAdapter.java 30 Nov 2003 04:58:19 -0000 1.10 *************** *** 228,232 **** } else if (sf instanceof FeatureSetI) { FeatureSetI fs = (FeatureSetI)sf; ! SequenceI seq = fs.getAlignmentSequence(); if (seq != null) { name = seq.getDisplayId(); --- 228,232 ---- } else if (sf instanceof FeatureSetI) { FeatureSetI fs = (FeatureSetI)sf; ! SequenceI seq = fs.getHitSequence(); if (seq != null) { name = seq.getDisplayId(); |