X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=847453fdf54d135f8e601f5a4048e02bd7f5c4ee;hb=a0d3647da9f02df7c5a13f59e5db552e7567974f;hp=77755f8d06fe1b42ae03bb09267da5d30e1336be;hpb=a08304fdd7bca01ea5520a7a032d512f285ebbca;p=jalview.git
diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 77755f8..847453f 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,23 +1,27 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
import java.io.IOException;
+import java.util.Hashtable;
import java.util.Map;
import org.jmol.api.JmolStatusListener;
@@ -38,6 +42,7 @@ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.util.MessageManager;
/**
* Import and process PDB files with Jmol
@@ -53,12 +58,10 @@ public class PDBFileWithJmol extends AlignFile implements
Viewer viewer = null;
- public PDBFileWithJmol(String inFile, String type)
- throws IOException
+ public PDBFileWithJmol(String inFile, String type) throws IOException
{
super(inFile, type);
}
-
public PDBFileWithJmol(FileParse fp) throws IOException
{
@@ -93,10 +96,7 @@ public class PDBFileWithJmol extends AlignFile implements
jmolApp.startViewer(viewer, null);
} catch (ClassCastException x)
{
- throw new Error(
- "Jmol version "
- + JmolViewer.getJmolVersion()
- + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
+ throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
x);
}
}
@@ -155,7 +155,7 @@ public class PDBFileWithJmol extends AlignFile implements
{
char newseq[] = new char[len];
System.arraycopy(seq, 0, newseq, 0, len);
- Annotation asecstr[] = new Annotation[len];
+ Annotation asecstr[] = new Annotation[len+firstrnum-1];
for (int p = 0; p < len; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
@@ -171,13 +171,24 @@ public class PDBFileWithJmol extends AlignFile implements
pdbe.setFile(getDataName());
pdbe.setId(getDataName());
sq.addPDBId(pdbe);
+ pdbe.setProperty(new Hashtable());
+ pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+ // JAL-1533
+ // Need to put the number of models for this polymer somewhere for Chimera/others to grab
+ // pdbe.getProperty().put("PDBMODELS", biopoly.)
seqs.add(sq);
if (!(biopoly.isDna() || biopoly.isRna()))
{
AlignmentAnnotation ann = new AlignmentAnnotation(
"Secondary Structure",
"Secondary Structure from PDB File", asecstr);
+ ann.belowAlignment=true;
+ ann.visible=true;
+ ann.autoCalculated=false;
+ ann.setCalcId(getClass().getName());
sq.addAlignmentAnnotation(ann);
+ ann.adjustForAlignment();
+ ann.validateRangeAndDisplay();
annotations.add(ann);
}
}