/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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/>.
*/
package jalview.bin;
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AppletJmol;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.appletgui.FeatureSettings;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.io.IdentifyFile;
+import jalview.io.JnetAnnotationMaker;
+
+import java.applet.Applet;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import java.lang.reflect.Method;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Jalview Applet. Runs in Java 1.18 runtime
// //////////////////////////////////////////////
// //////////////////////////////////////////////
- static int lastFrameX = 200;
+ public static int lastFrameX = 200;
- static int lastFrameY = 200;
+ public static int lastFrameY = 200;
boolean fileFound = true;
private boolean checkForJmol = true;
private boolean checkedForJmol = false; // ensure we don't check for jmol
- // every time the app is re-inited
+
+ // every time the app is re-inited
public boolean jmolAvailable = false;
+ private boolean alignPdbStructures=false;
+
public static boolean debug = false;
static String builddate = null, version = null;
}
if (debug)
{
-
- System.err.println("JalviewLite Version "+getVersion());
- System.err.println("Build Date : "+getBuildDate());
-
+
+ System.err.println("JalviewLite Version " + getVersion());
+ System.err.println("Build Date : " + getBuildDate());
+
}
/**
* if true disable the check for jmol
ex.printStackTrace();
}
}
-
+ /*
+ * <param name="alignpdbfiles" value="false/true"/>
+ * Undocumented for 2.6 - related to JAL-434
+ */
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",false));
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
*
* <param name="PDBfile3" value="1q0o Q45135_9MICO">
*/
-
+
int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if alignPdbStructures is true)
+ Vector pdbs=new Vector();
do
{
if (pdbFileCount > 0)
// the local pdb file was identified in the class loader
protocol = AppletFormatAdapter.URL; // this is probably NOT
// CORRECT!
- param = addProtocol(param); //
+ param = addProtocol(param); //
}
pdb.setFile(param);
}
}
}
-
- if (jmolAvailable)
- {
- new jalview.appletgui.AppletJmol(pdb, seqs, chains,
- newAlignFrame.alignPanel, protocol);
- lastFrameX += 40;
- lastFrameY += 40;
+
+ if (!alignPdbStructures) {
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ } else {
+ pdbs.addElement(new Object[] { pdb, seqs, chains, new String(protocol)});
}
- else
- new MCview.AppletPDBViewer(pdb, seqs, chains,
- newAlignFrame.alignPanel, protocol);
}
}
pdbFileCount++;
} while (pdbFileCount < 10);
-
+ if (pdbs.size()>0)
+ {
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+ String[][] chains = new String[pdbs.size()][];
+ String[] protocols = new String[pdbs.size()];
+ for (int pdbsi=0,pdbsiSize=pdbs.size(); pdbsi<pdbsiSize;pdbsi++)
+ {
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, protocols);
+
+ }
// ///////////////////////////
// modify display of features
//
public String arrayToSeparatorList(String[] list)
{
StringBuffer v = new StringBuffer();
- if (list != null)
+ if (list != null && list.length>0)
{
for (int i = 0, iSize = list.length - 1; i < iSize; i++)
{
}
return false;
}
+
+ /**
+ * bind a pdb file to a sequence in the given alignFrame.
+ *
+ * @param alFrame
+ * - null or specific alignFrame. This specifies the dataset that
+ * will be searched for a seuqence called sequenceId
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or seqeunceId location
+ * fails.
+ */
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ }
+
+ protected void setAlignPdbStructures(boolean alignPdbStructures)
+ {
+ this.alignPdbStructures = alignPdbStructures;
+ }
+
+ public boolean isAlignPdbStructures()
+ {
+ return alignPdbStructures;
+ }
+
+ /**
+ * get all components associated with the applet of the given type
+ * @param class1
+ * @return
+ */
+ public Vector getAppletWindow(Class class1)
+ {
+ Vector wnds = new Vector();
+ Component[] cmp = getComponents();
+ if (cmp!=null)
+ {
+ for (int i=0;i<cmp.length;i++)
+ {
+ if (class1.isAssignableFrom(cmp[i].getClass()))
+ {
+ wnds.addElement(cmp);
+ }
+ }}
+ return wnds;
+ }
+
+
+ /**
+ * bind structures in a viewer to any matching sequences in an alignFrame (use
+ * sequenceIds to limit scope of search to specific sequences)
+ *
+ * @param alFrame
+ * @param viewer
+ * @param sequenceIds
+ * @return TODO: consider making an exception structure for indicating when
+ * binding fails
+ public SequenceStructureBinding addStructureViewInstance(
+ AlignFrame alFrame, Object viewer, String sequenceIds)
+ {
+
+ if (sequenceIds != null && sequenceIds.length() > 0)
+ {
+ return alFrame.addStructureViewInstance(viewer,
+ separatorListToArray(sequenceIds));
+ }
+ else
+ {
+ return alFrame.addStructureViewInstance(viewer, null);
+ }
+ // return null;
+ }
+ */
}
git://source.jalview.org / jalview.git / blobdiff