/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
{\r
anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(\r
ae[aa].getDisplayCharacter(), ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().charAt(0), ae[aa]\r
- .getValue());\r
+ ae[aa].getSecondaryStructure().charAt(0),\r
+ ae[aa].getValue());\r
}\r
\r
jalview.datamodel.AlignmentAnnotation jaa = null;\r
\r
for (int i = 0; i < JSEQ.length; i++)\r
{\r
- af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
+ af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),\r
new java.awt.Color(JSEQ[i].getColour()));\r
}\r
\r
groups[i].getDisplayText(), groups[i].getColourText(),\r
groups[i].getStart(), groups[i].getEnd());\r
\r
- sg\r
- .setOutlineColour(new java.awt.Color(groups[i]\r
- .getOutlineColour()));\r
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));\r
\r
if (groups[i].getConsThreshold() != 0)\r
{\r
jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
- "All", ResidueProperties.propHash, 3, sg\r
- .getSequences(null), 0, sg.getWidth() - 1);\r
+ "All", ResidueProperties.propHash, 3,\r
+ sg.getSequences(null), 0, sg.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, 25);\r
sg.cs.setConservation(c);\r
}\r
}\r
\r
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view\r
- .getHeight());\r
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
+ view.getHeight());\r
af.viewport.setStartRes(view.getStartRes());\r
af.viewport.setStartSeq(view.getStartSeq());\r
af.viewport.setShowAnnotation(view.getShowAnnotation());\r
if (cs != null)\r
{\r
cs.setThreshold(view.getPidThreshold(), true);\r
- cs.setConsensus(af.viewport.hconsensus);\r
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());\r
}\r
}\r
\r
\r
af.setMenusFromViewport(af.viewport);\r
\r
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view\r
- .getHeight());\r
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),\r
+ view.getHeight());\r
\r
// LOAD TREES\r
// /////////////////////////////////////\r
\r
Tree tree = jms.getTree(t);\r
\r
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree\r
- .getNewick()), tree.getTitle(), tree.getWidth(), tree\r
- .getHeight(), tree.getXpos(), tree.getYpos());\r
+ TreePanel tp = af.ShowNewickTree(\r
+ new jalview.io.NewickFile(tree.getNewick()),\r
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),\r
+ tree.getXpos(), tree.getYpos());\r
\r
tp.fitToWindow.setState(tree.getFitToWindow());\r
tp.fitToWindow_actionPerformed(null);\r