X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=7d578869b93fb697a661df4320095243ae040553;hb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;hp=e77a23c55b0a47e61219bd2db8c58735bd2860fb;hpb=43b415c68805f3dec44a6ddc666d52220483c120;p=jalview.git
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index e77a23c..7d57886 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,20 +1,51 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structures.models;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
/**
*
* A base class to hold common function for protein structure model binding.
@@ -31,6 +62,10 @@ public abstract class AAStructureBindingModel extends
private StructureSelectionManager ssm;
+ /*
+ * distinct PDB entries (pdb files) associated
+ * with sequences
+ */
private PDBEntry[] pdbEntry;
/*
@@ -46,12 +81,21 @@ public abstract class AAStructureBindingModel extends
/*
* datasource protocol for access to PDBEntrylatest
*/
- String protocol = null;
+ DataSourceType protocol = null;
protected boolean colourBySequence = true;
private boolean nucleotide;
+ private boolean finishedInit = false;
+
+ /**
+ * current set of model filenames loaded in the Jmol instance
+ */
+ protected String[] modelFileNames = null;
+
+ public String fileLoadingError;
+
/**
* Data bean class to simplify parameterisation in superposeStructures
*/
@@ -104,19 +148,14 @@ public abstract class AAStructureBindingModel extends
* @param protocol
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
this.ssm = ssm;
this.sequence = sequenceIs;
this.nucleotide = Comparison.isNucleotide(sequenceIs);
- this.chains = chains;
this.pdbEntry = pdbentry;
this.protocol = protocol;
- if (chains == null)
- {
- this.chains = new String[pdbentry.length][];
- }
}
public StructureSelectionManager getSsm()
@@ -176,7 +215,7 @@ public abstract class AAStructureBindingModel extends
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
@@ -200,7 +239,9 @@ public abstract class AAStructureBindingModel extends
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
- * @param viewerName TODO
+ *
+ * @param viewerName
+ * TODO
* @param verbose
*
* @return
@@ -208,33 +249,28 @@ public abstract class AAStructureBindingModel extends
public String getViewerTitle(String viewerName, boolean verbose)
{
if (getSequence() == null || getSequence().length < 1
- || getPdbCount() < 1
- || getSequence()[0].length < 1)
+ || getPdbCount() < 1 || getSequence()[0].length < 1)
{
return ("Jalview " + viewerName + " Window");
}
// TODO: give a more informative title when multiple structures are
// displayed.
StringBuilder title = new StringBuilder(64);
- final PDBEntry pdbEntry = getPdbEntry(0);
+ final PDBEntry pdbe = getPdbEntry(0);
title.append(viewerName + " view for " + getSequence()[0][0].getName()
- + ":"
- + pdbEntry.getId());
-
+ + ":" + pdbe.getId());
+
if (verbose)
{
- if (pdbEntry.getProperty() != null)
+ String method = (String) pdbe.getProperty("method");
+ if (method != null)
{
- if (pdbEntry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbEntry.getProperty().get("method"));
- }
- if (pdbEntry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbEntry.getProperty().get("chains"));
- }
+ title.append(" Method: ").append(method);
+ }
+ String chain = (String) pdbe.getProperty("chains");
+ if (chain != null)
+ {
+ title.append(" Chain:").append(chain);
}
}
return title.toString();
@@ -266,8 +302,7 @@ public abstract class AAStructureBindingModel extends
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_no_pdbentry_from_index",
- new Object[]
- { Integer.valueOf(pe).toString() }));
+ new Object[] { Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
List s = new ArrayList();
@@ -337,8 +372,8 @@ public abstract class AAStructureBindingModel extends
*
* @returns the pdb entries added to the current set.
*/
- public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
- String[][] chns)
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
{
List v = new ArrayList();
List rtn = new ArrayList();
@@ -351,8 +386,7 @@ public abstract class AAStructureBindingModel extends
int r = v.indexOf(pdbe[i]);
if (r == -1 || r >= getPdbCount())
{
- rtn.add(new int[]
- { v.size(), i });
+ rtn.add(new int[] { v.size(), i });
v.add(pdbe[i]);
}
else
@@ -489,18 +523,22 @@ public abstract class AAStructureBindingModel extends
* the sequence alignment which is the basis of structure
* superposition
* @param matched
- * an array of booleans, indexed by alignment column, where true
- * indicates that every structure has a mapped residue present in the
- * column (so the column can participate in structure alignment)
+ * a BitSet, where bit j is set to indicate that every structure has
+ * a mapped residue present in column j (so the column can
+ * participate in structure alignment)
* @param structures
* an array of data beans corresponding to pdb file index
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- boolean[] matched, SuperposeData[] structures)
+ BitSet matched, SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getPdbFile();
+ if (files == null)
+ {
+ return -1;
+ }
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
@@ -523,16 +561,16 @@ public abstract class AAStructureBindingModel extends
{
refStructure = pdbfnum;
}
- for (int r = 0; r < matched.length; r++)
+ for (int r = 0; r < alignment.getWidth(); r++)
{
- if (!matched[r])
+ if (!matched.get(r))
{
continue;
}
int pos = getMappedPosition(theSequence, r, mapping);
if (pos < 1 || pos == lastPos)
{
- matched[r] = false;
+ matched.clear(r);
continue;
}
lastPos = pos;
@@ -545,7 +583,11 @@ public abstract class AAStructureBindingModel extends
}
structures[pdbfnum].pdbId = mapping.getPdbId();
structures[pdbfnum].isRna = theSequence.getRNA() != null;
- // move on to next pdb file
+
+ /*
+ * move on to next pdb file (ignore sequences for other chains
+ * for the same structure)
+ */
s = seqCountForPdbFile;
break;
}
@@ -578,6 +620,10 @@ public abstract class AAStructureBindingModel extends
for (String file : files)
{
notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
try
{
StructureMapping[] sm = getSsm().getMapping(file);
@@ -613,7 +659,10 @@ public abstract class AAStructureBindingModel extends
{
for (SequenceI s : seqs)
{
- if (s == seq)
+ if (s == seq
+ || (s.getDatasetSequence() != null && s
+ .getDatasetSequence() == seq
+ .getDatasetSequence()))
{
return true;
}
@@ -623,4 +672,122 @@ public abstract class AAStructureBindingModel extends
}
return false;
}
-}
\ No newline at end of file
+
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean fi)
+ {
+ this.finishedInit = fi;
+ }
+
+ /**
+ * Returns a list of chains mapped in this viewer.
+ *
+ * @return
+ */
+ public abstract List getChainNames();
+
+ /**
+ * Returns the Jalview panel hosting the structure viewer (if any)
+ *
+ * @return
+ */
+ public JalviewStructureDisplayI getViewer()
+ {
+ return null;
+ }
+
+ public abstract void setJalviewColourScheme(ColourSchemeI cs);
+
+ /**
+ * Constructs and sends a command to align structures against a reference
+ * structure, based on one or more sequence alignments. May optionally return
+ * an error or warning message for the alignment command.
+ *
+ * @param alignments
+ * an array of alignments to process
+ * @param structureIndices
+ * 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
+ * @return
+ */
+ public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
+ ColumnSelection[] hiddenCols);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignViewportI alignViewportI);
+
+ /**
+ * returns the current featureRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+
+ /**
+ * returns the current sequenceRenderer that should be used to colour the
+ * structures
+ *
+ * @param alignment
+ *
+ * @return
+ */
+ public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+
+ protected abstract void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands);
+
+ public abstract void colourByChain();
+
+ public abstract void colourByCharge();
+
+ /**
+ * colour any structures associated with sequences in the given alignment
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
+ * if colourBySequence is enabled.
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv)
+ {
+ if (!colourBySequence || !isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getPdbFile();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
+
+ FeatureRenderer fr = null;
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (showFeatures)
+ {
+ fr = getFeatureRenderer(alignmentv);
+ }
+
+ StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, sr, fr, alignmentv.getAlignViewport());
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
+}