X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=60f7ec9d05e26e8b08081974d1ca2b589b3a8fdb;hb=21d6c27e237d77ae258755562aa8abdc6b5320b8;hp=584c076395e7f55fed25ba1be38e78062e6380d3;hpb=f8456d4c0b253ae32a4b569e12bb8bf7f7096d65;p=jalview.git diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java old mode 100755 new mode 100644 index 584c076..60f7ec9 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -124,7 +124,7 @@ public class PDBCanvas extends JPanel implements MouseListener, this.pdbentry = pdbentry; this.sequence = seq; - ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm = ap.av.getStructureSelectionManager(); try { @@ -173,8 +173,8 @@ public class PDBCanvas extends JPanel implements MouseListener, // Now lets compare the sequences to get // the start and end points. // Align the sequence to the pdb - AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains - .elementAt(i)).sequence, "pep"); + AlignSeq as = new AlignSeq(sequence, + ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep"); as.calcScoreMatrix(); as.traceAlignment(); PrintStream ps = new PrintStream(System.out) @@ -1069,7 +1069,8 @@ public class PDBCanvas extends JPanel implements MouseListener, // /StructureListener public String[] getPdbFile() { - return new String[] { pdbentry.getFile() }; + return new String[] + { pdbentry.getFile() }; } String lastMessage; @@ -1156,4 +1157,11 @@ public class PDBCanvas extends JPanel implements MouseListener, repaint(); } + @Override + public void releaseReferences(Object svl) + { + // TODO Auto-generated method stub + + } + }