*/
package jalview.ext.rbvi.chimera;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.httpserver.AbstractRequestHandler;
import java.io.PrintWriter;
import java.net.BindException;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
}
/**
- * Construct and send a command to align structures against a reference
- * structure, based on one or more sequence alignments
- *
- * @param _alignment
- * an array of alignments to process
- * @param _refStructure
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param _hiddenCols
- * an array of corresponding hidden columns for each alignment
+ * {@inheritDoc}
*/
@Override
- public void superposeStructures(AlignmentI[] _alignment,
+ public String superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
StringBuilder allComs = new StringBuilder(128);
if (!waitForFileLoad(files))
{
- return;
+ return null;
}
refreshPdbEntries();
}
/*
- * 'matched' array will hold 'true' for visible alignment columns where
+ * 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to the PDB structure
*/
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
SuperposeData[] structures = new SuperposeData[files.length];
refStructure = candidateRefStructure;
}
- int nmatched = 0;
- for (boolean b : matched)
- {
- if (b)
- {
- nmatched++;
- }
- }
+ int nmatched = matched.cardinality();
if (nmatched < 4)
{
- // TODO: bail out here because superposition illdefined?
+ return MessageManager.formatMessage("label.insufficient_residues",
+ nmatched);
}
/*
int lpos = -1;
boolean run = false;
StringBuilder molsel = new StringBuilder();
- for (int r = 0; r < matched.length; r++)
+
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
{
- if (matched[r])
+ int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
+ if (lpos != pdbResNum - 1)
{
- int pdbResNum = structures[pdbfnum].pdbResNo[r];
- if (lpos != pdbResNum - 1)
+ /*
+ * discontiguous - append last residue now
+ */
+ if (lpos != -1)
{
- /*
- * discontiguous - append last residue now
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- molsel.append(chainCd);
- molsel.append(",");
- }
- run = false;
+ molsel.append(String.valueOf(lpos));
+ molsel.append(chainCd);
+ molsel.append(",");
}
- else
+ run = false;
+ }
+ else
+ {
+ /*
+ * extending a contiguous run
+ */
+ if (!run)
{
/*
- * extending a contiguous run
+ * start the range selection
*/
- if (!run)
- {
- /*
- * start the range selection
- */
- molsel.append(String.valueOf(lpos));
- molsel.append("-");
- }
- run = true;
+ molsel.append(String.valueOf(lpos));
+ molsel.append("-");
}
- lpos = pdbResNum;
+ run = true;
}
+ lpos = pdbResNum;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
/*
.append(";" + command.toString());
}
}
+
+ String error = null;
if (selectioncom.length() > 0)
{
// TODO: visually distinguish regions that were superposed
}
allComs.append("; ~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString()).append("; focus");
- sendChimeraCommand(allComs.toString(), false);
+ List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
+ true);
+ for (String reply : chimeraReplies)
+ {
+ if (reply.toLowerCase().contains("unequal numbers of atoms"))
+ {
+ error = reply;
+ }
+ }
}
-
+ return error;
}
/**
* @param files
* @param sr
* @param fr
- * @param alignment
+ * @param viewport
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ AlignViewportI viewport)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, alignment);
+ getSequence(), sr, fr, viewport);
}
/**
* features visible in Jalview
*
* @param avp
+ * @return
*/
- public void sendFeaturesToViewer(AlignmentViewPanel avp)
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
// TODO refactor as required to pull up to an interface
AlignmentI alignment = avp.getAlignment();
*/
if (fr == null)
{
- return;
+ return 0;
}
String[] files = getPdbFile();
if (files == null)
{
- return;
+ return 0;
}
StructureMappingcommandSet commandSet = ChimeraCommands
sendAsynchronousCommand(command, null);
}
}
+ return commands.length;
}
/**
/*
* locate the mapped position in the alignment (if any)
*/
- SearchResults sr = getSsm()
+ SearchResultsI sr = getSsm()
.findAlignmentPositionsForStructurePositions(atoms);
/*
git://source.jalview.org / jalview.git / blobdiff