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Merge branch 'Release_2_8_2_Branch_i18n' into Release_2_8_2_Branch
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
PDBFileWithJmol.java
diff --git
a/src/jalview/ext/jmol/PDBFileWithJmol.java
b/src/jalview/ext/jmol/PDBFileWithJmol.java
index
77755f8
..
847453f
100644
(file)
--- 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
*
* 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.
*
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
import java.io.IOException;
*/
package jalview.ext.jmol;
import java.io.IOException;
+import java.util.Hashtable;
import java.util.Map;
import org.jmol.api.JmolStatusListener;
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.datamodel.SequenceI;
import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.util.MessageManager;
/**
* Import and process PDB files with Jmol
/**
* Import and process PDB files with Jmol
@@
-53,12
+58,10
@@
public class PDBFileWithJmol extends AlignFile implements
Viewer viewer = null;
Viewer viewer = null;
- public PDBFileWithJmol(String inFile, String type)
- throws IOException
+ public PDBFileWithJmol(String inFile, String type) throws IOException
{
super(inFile, type);
}
{
super(inFile, type);
}
-
public PDBFileWithJmol(FileParse fp) throws IOException
{
public PDBFileWithJmol(FileParse fp) throws IOException
{
@@
-93,10
+96,7
@@
public class PDBFileWithJmol extends AlignFile implements
jmolApp.startViewer(viewer, null);
} catch (ClassCastException x)
{
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);
}
}
x);
}
}
@@
-155,7
+155,7
@@
public class PDBFileWithJmol extends AlignFile implements
{
char newseq[] = new char[len];
System.arraycopy(seq, 0, newseq, 0, len);
{
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')
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.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);
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);
sq.addAlignmentAnnotation(ann);
+ ann.adjustForAlignment();
+ ann.validateRangeAndDisplay();
annotations.add(ann);
}
}
annotations.add(ann);
}
}