X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=0b19d51b7c74ac68502deba4ab4779ef17f532fe;hb=a5e22141bc3185284588761a69f023d527e7f18e;hp=3c4041413282c840e9631e2262e086c21321cbd1;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 3c40414..0b19d51 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,20 +1,53 @@
+/*
+ * 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 jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRendererI;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.SequenceRenderer;
+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;
+import org.springframework.web.filter.ShallowEtagHeaderFilter;
+
/**
*
* A base class to hold common function for protein structure model binding.
@@ -24,13 +57,37 @@ import java.util.List;
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
+ public enum ColourBy
+ {
+ Sequence, Chain, ChargeAndCysteine, Jalview, Viewer
+ }
+ /*
+ * selected colour menu option
+ */
+ private ColourBy colourBy = ColourBy.Sequence;
+
+ /*
+ * selected colour scheme, if a Jalview colour scheme is selected
+ */
+ private ColourSchemeI colourScheme;
+
+ /*
+ * flag for whether to include feature colouring, if using a Jalview colour
+ * scheme (independently of whether features are shown on alignment)
+ */
+ private boolean showFeatures;
+
private StructureSelectionManager ssm;
+ /*
+ * distinct PDB entries (pdb files) associated
+ * with sequences
+ */
private PDBEntry[] pdbEntry;
/*
@@ -46,15 +103,20 @@ public abstract class AAStructureBindingModel extends
/*
* datasource protocol for access to PDBEntrylatest
*/
- String protocol = null;
-
- protected boolean colourBySequence = true;
-
+ DataSourceType protocol = null;
+
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
*/
protected class SuperposeData
@@ -102,25 +164,71 @@ public abstract class AAStructureBindingModel extends
* @param ssm
* @param pdbentry
* @param sequenceIs
- * @param chains
* @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)
+ resolveChains();
+ }
+
+ private boolean resolveChains()
+ {
+ /**
+ * final count of chain mappings discovered
+ */
+ int chainmaps = 0;
+ // JBPNote: JAL-2693 - this should be a list of chain mappings per
+ // [pdbentry][sequence]
+ String[][] newchains = new String[pdbEntry.length][];
+ int pe = 0;
+ for (PDBEntry pdb : pdbEntry)
{
- this.chains = new String[pdbentry.length][];
+ SequenceI[] seqsForPdb = sequence[pe];
+ if (seqsForPdb != null)
+ {
+ newchains[pe] = new String[seqsForPdb.length];
+ int se = 0;
+ for (SequenceI asq : seqsForPdb)
+ {
+ String chain = (chains != null && chains[pe] != null)
+ ? chains[pe][se]
+ : null;
+ SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+ : asq.getDatasetSequence();
+ if (sq.getAllPDBEntries() != null)
+ {
+ for (PDBEntry pdbentry : sq.getAllPDBEntries())
+ {
+ if (pdb.getFile() != null && pdbentry.getFile() != null
+ && pdb.getFile().equals(pdbentry.getFile()))
+ {
+ String chaincode = pdbentry.getChainCode();
+ if (chaincode != null && chaincode.length() > 0)
+ {
+ chain = chaincode;
+ chainmaps++;
+ break;
+ }
+ }
+ }
+ }
+ newchains[pe][se] = chain;
+ se++;
+ }
+ pe++;
+ }
}
- }
+ chains = newchains;
+ return chainmaps > 0;
+ }
public StructureSelectionManager getSsm()
{
return ssm;
@@ -178,7 +286,7 @@ public abstract class AAStructureBindingModel extends
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
@@ -219,24 +327,21 @@ public abstract class AAStructureBindingModel extends
// 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();
@@ -251,14 +356,19 @@ public abstract class AAStructureBindingModel extends
}
+ public void setColourBy(ColourBy option)
+ {
+ colourBy = option;
+ }
+
public boolean isColourBySequence()
{
- return colourBySequence;
+ return colourBy == ColourBy.Sequence;
}
-
- public void setColourBySequence(boolean colourBySequence)
+
+ protected boolean isJalviewColourScheme()
{
- this.colourBySequence = colourBySequence;
+ return colourBy == ColourBy.Jalview;
}
protected void addSequenceAndChain(int pe, SequenceI[] seq,
@@ -268,7 +378,8 @@ 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();
@@ -489,18 +600,22 @@ 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();
+ String[] files = getStructureFiles();
+ if (files == null)
+ {
+ return -1;
+ }
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
@@ -523,16 +638,16 @@ 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 +660,11 @@ 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 +697,10 @@ public abstract class AAStructureBindingModel extends
for (String file : files)
{
notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
try
{
StructureMapping[] sm = getSsm().getMapping(file);
@@ -594,8 +717,8 @@ public abstract class AAStructureBindingModel extends
if (waiting)
{
- System.err
- .println("Timed out waiting for structure viewer to load file "
+ System.err.println(
+ "Timed out waiting for structure viewer to load file "
+ notLoaded);
return false;
}
@@ -613,7 +736,8 @@ public abstract class AAStructureBindingModel extends
{
for (SequenceI s : seqs)
{
- if (s == seq)
+ if (s == seq || (s.getDatasetSequence() != null
+ && s.getDatasetSequence() == seq.getDatasetSequence()))
{
return true;
}
@@ -633,4 +757,166 @@ public abstract class AAStructureBindingModel extends
{
this.finishedInit = fi;
}
-}
\ No newline at end of file
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the selected colour scheme, possibly with reference to the given
+ * alignment view
+ *
+ * @param cs
+ * @param ap
+ * @param showFeats
+ */
+ public void setJalviewColourScheme(ColourSchemeI cs, AlignmentViewPanel ap,
+ boolean showFeats)
+ {
+ colourBy = ColourBy.Jalview;
+ colourScheme = cs;
+ showFeatures = showFeats;
+
+ if (!showFeats && (cs == null || cs.isSimple()))
+ {
+ setSimpleColourScheme(cs);
+ }
+ else
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(), cs), showFeatures);
+ }
+ }
+
+ /**
+ * Sets a colour scheme which is determined solely by the residue at each
+ * position
+ *
+ * @param cs
+ */
+ protected abstract void setSimpleColourScheme(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, HiddenColumns[] hiddenCols);
+
+ public abstract void setBackgroundColour(Color col);
+
+ protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRendererI sr, AlignmentViewPanel avp, boolean showFeatures);
+
+ protected abstract void colourBySequence(
+ StructureMappingcommandSet[] colourBySequenceCommands);
+
+ public void colourByChain()
+ {
+ colourBy = ColourBy.Chain;
+ }
+
+ public void colourByCharge()
+ {
+ colourBy = ColourBy.ChargeAndCysteine;
+ }
+
+ public void colourBySequence(AlignmentViewPanel alignmentv, boolean showFeatures)
+ {
+ colourBySequence(alignmentv, alignmentv.getSequenceRenderer(), showFeatures);
+ }
+
+ /**
+ * Colours any structures associated with sequences in the given alignment view
+ * using the getFeatureRenderer() and getSequenceRenderer() renderers
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv, SequenceRendererI sr, boolean showFeats)
+ {
+ showFeatures = showFeats;
+ if (!isLoadingFinished())
+ {
+ return;
+ }
+ if (getSsm() == null)
+ {
+ return;
+ }
+ String[] files = getStructureFiles();
+
+ StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
+ files, sr, alignmentv, showFeatures);
+ colourBySequence(colourBySequenceCommands);
+ }
+
+ public boolean hasFileLoadingError()
+ {
+ return fileLoadingError != null && fileLoadingError.length() > 0;
+ }
+
+ public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
+
+@Override
+public void updateColours(Object source) {
+ AlignmentPanel ap = (AlignmentPanel) source;
+
+ /*
+ * ignore events from panels not used to colour this view
+ */
+ if (!getViewer().isUsedForColourBy(ap))
+ {
+ return;
+ }
+
+ /*
+ * no need to update colours if structure colouring is not
+ * viewport dependent
+ */
+ if (!isColourBySequence() && !isJalviewColourScheme())
+ {
+ return;
+ }
+ if (!showFeatures && (colourScheme == null || colourScheme.isSimple()))
+ {
+ return;
+ }
+
+ if (!isLoadingFromArchive())
+ {
+ if (isColourBySequence())
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport()),
+ showFeatures);
+ }
+ else
+ {
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(),
+ colourScheme), showFeatures);
+ }
+ }
+ }
+}