From 9061d32af38c944b1d553ab4fd7c0afba5b6c654 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 27 Aug 2010 11:34:50 +0000 Subject: [PATCH] revised sequence/structure binding so one structure associated with x-seuqenceI's --- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/appletgui/AppletJmolBinding.java | 4 ++-- src/jalview/appletgui/ExtJmol.java | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 8606e22..3707cfa 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -104,7 +104,7 @@ public class AppletJmol extends EmbmenuFrame implements { this.ap = ap; jmb = new AppletJmolBinding(this, new PDBEntry[] - { pdbentry }, seq, chains, protocol); + { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java index 9299af2..3afa805 100644 --- a/src/jalview/appletgui/AppletJmolBinding.java +++ b/src/jalview/appletgui/AppletJmolBinding.java @@ -18,8 +18,8 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding */ private AppletJmol appletJmolBinding; - public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq, - String[] chains, String protocol) + public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq, + String[][] chains, String protocol) { super(pdbentry, seq, chains, protocol); appletJmolBinding = appletJmol; diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java index 8e42f2a..53c2f1c 100644 --- a/src/jalview/appletgui/ExtJmol.java +++ b/src/jalview/appletgui/ExtJmol.java @@ -22,14 +22,14 @@ public class ExtJmol extends JalviewJmolBinding private AlignmentPanel ap; - protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[] seq, String[] chains, + protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains, String protocol) { super(pdbentry, seq, chains, protocol); } public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel, - SequenceI[] seqs) + SequenceI[][] seqs) { super(viewer); ap = alignPanel; -- 1.7.10.2