From 4065be0b102659a046a75ac1c8902d9a8086d63b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 10 Feb 2015 15:35:48 +0000 Subject: [PATCH] JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought --- src/jalview/gui/AlignViewport.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 6ea8df1..638d3e5 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1000,6 +1000,10 @@ public class AlignViewport extends AlignmentViewport implements { // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + // JBPComment: title is a largely redundant parameter at the moment + // JBPComment: this really should be an 'insert/pre/append' controller + // JBPComment: but the DNA/Protein check makes it a bit more complex + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with // this comment: // TODO: create undo object for this JAL-1101 @@ -1010,6 +1014,7 @@ public class AlignViewport extends AlignmentViewport implements */ if (getAlignment().isNucleotide() != al.isNucleotide()) { + // TODO: JAL-845 try a bit harder to link up imported sequences final Set sequenceNames = getAlignment().getSequenceNames(); sequenceNames.retainAll(al.getSequenceNames()); if (!sequenceNames.isEmpty()) // at least one sequence name in both @@ -1020,6 +1025,8 @@ public class AlignViewport extends AlignmentViewport implements } } } + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence for (int i = 0; i < al.getHeight(); i++) { @@ -1027,6 +1034,8 @@ public class AlignViewport extends AlignmentViewport implements } // TODO this call was done by SequenceFetcher but not FileLoader or // CutAndPasteTransfer. Is it needed? + // JBPComment: this repositions the view to show the new sequences + // JBPComment: so it is needed for UX setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } -- 1.7.10.2