From 4741fc6fc72b7c5ffd75af5b1bc17070fef448f9 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 7 May 2007 13:57:03 +0000 Subject: [PATCH] Dont use gold colouring for highlight --- src/MCview/AppletPDBCanvas.java | 9 +++------ src/jalview/appletgui/AppletJmol.java | 11 ++++++----- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index bfcd67a..e11e558 100755 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -118,7 +118,6 @@ public class AppletPDBCanvas int pdbend = 0; int seqstart = 0; int seqend = 0; - AlignSeq maxAlignseq = null; //JUST DEAL WITH ONE SEQUENCE FOR NOW SequenceI sequence = seq[0]; @@ -165,8 +164,7 @@ public class AppletPDBCanvas pdbend = as.seq2end; seqstart = as.seq1start + sequence.getStart() - 1; seqend = as.seq1end + sequence.getEnd() - 1; - maxAlignseq = as; - } + } mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend); @@ -498,7 +496,7 @@ public class AppletPDBCanvas // Applet and Application specific sequence renderers to be used void colourBySequence() { - SequenceRenderer sr = ap.getSequenceRenderer(); + SequenceRenderer sr = new SequenceRenderer(ap.av); StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); @@ -1078,7 +1076,7 @@ public class AppletPDBCanvas ///StructureListener public String getPdbFile() { - return "???"; + return pdbentry.getFile(); } @@ -1159,7 +1157,6 @@ public class AppletPDBCanvas public void updateColours(Object source) { - AlignmentPanel ap = (AlignmentPanel) source; colourBySequence(); redrawneeded = true; repaint(); diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index f873230..14e6704 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -441,14 +441,15 @@ public class AppletJmol extends Frame resetLastRes.append(":" + chain); } - eval.append(";color gold;wireframe 100"); + eval.append(";wireframe 100");//;color gold Color col = new Color(viewer.getAtomArgb(atomIndex)); - resetLastRes.append(";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "];wireframe 0"); + resetLastRes.append(";wireframe 0;"//color[" + // + col.getRed() + "," + // + col.getGreen() + "," + // + col.getBlue() + "]" + ); viewer.evalStringQuiet(eval.toString()); -- 1.7.10.2