/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*/
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.api.SequenceStructureBinding;
-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
public boolean jmolAvailable = false;
+ private boolean alignPdbStructures = false;
+
public static boolean debug = false;
static String builddate = null, version = null;
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">
*/
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);
}
}
- newAlignFrame.newStructureView(applet, pdb, seqs, chains, protocol);
-
+ if (!alignPdbStructures)
+ {
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ }
+ else
+ {
+ pdbs.addElement(new Object[]
+ { pdb, seqs, chains, new String(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.
+ * 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)
+ 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;
+ }
+
/**
- * 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
+ * get all components associated with the applet of the given type
+ *
+ * @param class1
* @return
- * TODO: consider making an exception structure for indicating when binding fails
*/
- public SequenceStructureBinding addStructureViewInstance(AlignFrame alFrame, Object viewer, String sequenceIds)
+ public Vector getAppletWindow(Class class1)
{
- if (viewer!=null)
+ Vector wnds = new Vector();
+ Component[] cmp = getComponents();
+ if (cmp != null)
{
- if (sequenceIds!=null && sequenceIds.length()>0)
+ for (int i = 0; i < cmp.length; i++)
{
- return alFrame.addStructureViewInstance(viewer, separatorListToArray(sequenceIds));
- } else {
- return alFrame.addStructureViewInstance(viewer, null);
+ if (class1.isAssignableFrom(cmp[i].getClass()))
+ {
+ wnds.addElement(cmp);
+ }
}
}
- return null;
+ 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