From: Suzanna L. <su...@us...> - 2004-01-31 05:33:46
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Update of /cvsroot/gmod/apollo/src/java/apollo/gui/drawable In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19029/apollo/gui/drawable Modified Files: DrawableFeatureSet.java DrawableSeqFeature.java Log Message: for translational frame shift the drawing and the save and reading should be working same as above for readthrough of stop codon some questions remain on frame shift to see if final aa is present selection is now quite different. the selected item's source only indicates where the original select originated from. it does not imply anything about what views may contain representations of that selection. there is now a method in the views to return the sub-selection of the overall selection representing what features that view draws (inverts how this was previously done) removed some unused files. merged my sequenceedit class and the jalview one. michele and i independently created classes that were identical. very cute and gratifying to discover. selectfeature should now automatically scroll add a new annotation change event REPLACE. this should be useful when we get to implimenting undo. now in the annotation text editor if the changes are commited the cloned version simply replaces the older original version. the edits to account for sequencing errors on the genomic is still in the works. Index: DrawableFeatureSet.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/drawable/DrawableFeatureSet.java,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -d -r1.47 -r1.48 *** DrawableFeatureSet.java 26 Jan 2004 01:20:39 -0000 1.47 --- DrawableFeatureSet.java 29 Jan 2004 22:36:23 -0000 1.48 *************** *** 369,382 **** switch (ce.getType()) { case FeatureChangeEvent.REPLACE: if (parentOkay (parent, ce)) { ! deleteDrawable(parent); ! addFeatureDrawable(ce.getSecondFeature()); } else { System.err.println("Could not delete " + ce.getFirstFeature().getName() + " from " + ! getFeature().getName() + " because drawable was not found"); } case FeatureChangeEvent.ADD: case FeatureChangeEvent.MERGE: --- 369,386 ---- switch (ce.getType()) { case FeatureChangeEvent.REPLACE: + if (ce.getSubType() != AnnotationChangeEvent.COMMENT) { if (parentOkay (parent, ce)) { ! DrawableSetI grandparent = (DrawableSetI) parent.getRefDrawable(); ! grandparent.deleteDrawable(parent); ! grandparent.addFeatureDrawable(ce.getSecondFeature()); } else { System.err.println("Could not delete " + ce.getFirstFeature().getName() + " from " + ! parent.getRefDrawable().getName() + " because drawable was not found"); } + } + break; case FeatureChangeEvent.ADD: case FeatureChangeEvent.MERGE: Index: DrawableSeqFeature.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/drawable/DrawableSeqFeature.java,v retrieving revision 1.70 retrieving revision 1.71 diff -C2 -d -r1.70 -r1.71 *** DrawableSeqFeature.java 26 Jan 2004 14:24:43 -0000 1.70 --- DrawableSeqFeature.java 29 Jan 2004 22:36:23 -0000 1.71 *************** *** 453,457 **** position, 3, ! Color.gray); } } --- 453,457 ---- position, 3, ! Color.pink); } } |