From 30fbdf1d58c59dff55b3ba29c6135b2ad223383c Mon Sep 17 00:00:00 2001 From: jprocter Date: Sat, 8 Mar 2008 02:52:04 +0000 Subject: [PATCH] first hack to get true DNA and Sequence highlighting from Structure mouseovers --- .../structure/StructureSelectionManager.java | 93 +++++++++++++------- 1 file changed, 61 insertions(+), 32 deletions(-) diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index d33c380..e12e3ab 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -259,6 +259,7 @@ public class StructureSelectionManager public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) { + boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; SearchResults results = null; for (int i = 0; i < listeners.size(); i++) { @@ -267,41 +268,62 @@ public class StructureSelectionManager if (results == null) { results = new SearchResults(); - - for (int j = 0; j < mappings.length; j++) + } + int indexpos; + for (int j = 0; j < mappings.length; j++) + { + if (mappings[j].pdbfile.equals(pdbfile) + && mappings[j].pdbchain.equals(chain)) { - if (mappings[j].pdbfile.equals(pdbfile) - && mappings[j].pdbchain.equals(chain)) + indexpos = mappings[j].getSeqPos(pdbResNum); + results.addResult(mappings[j].sequence, indexpos, indexpos); + // construct highlighted sequence list + if (seqmappings!=null) { - results.addResult(mappings[j].sequence, mappings[j] - .getSeqPos(pdbResNum), mappings[j] - .getSeqPos(pdbResNum)); + + Enumeration e = seqmappings.elements(); + while (e.hasMoreElements()) + + { + ((AlignedCodonFrame) e.nextElement()).markMappedRegion( + mappings[j].sequence, indexpos, results); + } } } } - if (results.getSize() > 0) - { - ((SequenceListener) listeners.elementAt(i)) - .highlightSequence(results); - } - + } + } + if (results.getSize() > 0) + { + for (int i = 0; i < listeners.size(); i++) + { + Object li = listeners.elementAt(i); + if (li instanceof SequenceListener) + ((SequenceListener) li).highlightSequence(results); } } } Vector seqmappings = null; // should be a simpler list of mapped seuqence + /** * highlight regions associated with a position (indexpos) in seq - * @param seq the sequeence that the mouse over occured on - * @param indexpos the absolute position being mouseovered in seq (0 to seq.length()) - * @param index the sequence position (if -1, seq.findPosition is called to resolve the residue number) + * + * @param seq + * the sequeence that the mouse over occured on + * @param indexpos + * the absolute position being mouseovered in seq (0 to + * seq.length()) + * @param index + * the sequence position (if -1, seq.findPosition is called to + * resolve the residue number) */ public void mouseOverSequence(SequenceI seq, int indexpos, int index) { boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null; SearchResults results = null; - if (index==-1) - index=seq.findPosition(indexpos); + if (index == -1) + index = seq.findPosition(indexpos); StructureListener sl; int atomNo = 0; for (int i = 0; i < listeners.size(); i++) @@ -312,7 +334,8 @@ public class StructureSelectionManager for (int j = 0; j < mappings.length; j++) { - if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence()) + if (mappings[j].sequence == seq + || mappings[j].sequence == seq.getDatasetSequence()) { atomNo = mappings[j].getAtomNum(index); @@ -329,9 +352,9 @@ public class StructureSelectionManager if (relaySeqMappings && hasSequenceListeners && listeners.elementAt(i) instanceof SequenceListener) { - // DEBUG - //System.err.println("relay Seq " + seq.getDisplayId(false) + " " + - // index); + // DEBUG + // System.err.println("relay Seq " + seq.getDisplayId(false) + " " + + // index); if (results == null) { @@ -340,7 +363,7 @@ public class StructureSelectionManager { // construct highlighted sequence list - if (seqmappings!=null) + if (seqmappings != null) { Enumeration e = seqmappings.elements(); while (e.hasMoreElements()) @@ -369,11 +392,14 @@ public class StructureSelectionManager else if (listeners.elementAt(i) instanceof VamsasListener && !handlingVamsasMo) { - // DEBUG - //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " + + // DEBUG + // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " + // " + // index); - // pass the mouse over and absolute position onto the VamsasListener(s) - ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos); + // pass the mouse over and absolute position onto the + // VamsasListener(s) + ((VamsasListener) listeners.elementAt(i)) + .mouseOver(seq, indexpos); } } } @@ -384,23 +410,26 @@ public class StructureSelectionManager * handled */ boolean handlingVamsasMo = false; - long lastmsg=0; + + long lastmsg = 0; + /** * as mouseOverSequence but only route event to SequenceListeners * * @param sequenceI - * @param position in an alignment sequence + * @param position + * in an alignment sequence */ public void mouseOverVamsasSequence(SequenceI sequenceI, int position) { handlingVamsasMo = true; - long msg = sequenceI.hashCode()*(1+position); - if (lastmsg!=msg) + long msg = sequenceI.hashCode() * (1 + position); + if (lastmsg != msg) { lastmsg = msg; mouseOverSequence(sequenceI, position, -1); } - handlingVamsasMo = false; + handlingVamsasMo = false; } public Annotation[] colourSequenceFromStructure(SequenceI seq, -- 1.7.10.2