From b6d073bedc4b28e1a0e5a3a899cfb0e32349087e Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 5 Jun 2015 14:43:00 +0100 Subject: [PATCH] JAL-1622 code tidy only, no functional change --- .../structure/StructureSelectionManager.java | 132 +++++++++++--------- 1 file changed, 74 insertions(+), 58 deletions(-) diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 9702159..ef4a7a5 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -22,6 +22,7 @@ package jalview.structure; import java.io.PrintStream; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; import java.util.Enumeration; import java.util.HashMap; @@ -34,6 +35,7 @@ import java.util.Vector; import MCview.Atom; import MCview.PDBChain; +import MCview.PDBfile; import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; @@ -166,8 +168,9 @@ public class StructureSelectionManager * map between the PDB IDs (or structure identifiers) used by Jalview and the * absolute filenames for PDB data that corresponds to it */ - HashMap pdbIdFileName = new HashMap(), - pdbFileNameId = new HashMap(); + Map pdbIdFileName = new HashMap(); + + Map pdbFileNameId = new HashMap(); public void registerPDBFile(String idForFile, String absoluteFile) { @@ -204,8 +207,11 @@ public class StructureSelectionManager { if (instances != null) { - throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"), - new NullPointerException(MessageManager.getString("exception.ssm_context_is_null"))); + throw new Error( + MessageManager + .getString("error.implementation_error_structure_selection_manager_null"), + new NullPointerException(MessageManager + .getString("exception.ssm_context_is_null"))); } else { @@ -311,7 +317,7 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public MCview.PDBfile setMapping(SequenceI[] sequence, + synchronized public PDBfile setMapping(SequenceI[] sequence, String[] targetChains, String pdbFile, String protocol) { return setMapping(true, sequence, targetChains, pdbFile, protocol); @@ -335,15 +341,14 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public MCview.PDBfile setMapping(boolean forStructureView, - SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + synchronized public PDBfile setMapping(boolean forStructureView, + SequenceI[] sequence, String[] targetChains, String pdbFile, + String protocol) { /* * There will be better ways of doing this in the future, for now we'll use * the tried and tested MCview pdb mapping */ - MCview.PDBfile pdb = null; boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { @@ -362,8 +367,7 @@ public class StructureSelectionManager // false if any annotation present from this structure // JBPNote this fails for jmol/chimera view because the *file* is // passed, not the structure data ID - - if (MCview.PDBfile.isCalcIdForFile(ala, - findIdForPDBFile(pdbFile))) + if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) { parseSecStr = false; } @@ -371,10 +375,11 @@ public class StructureSelectionManager } } } + PDBfile pdb = null; try { - pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr, - secStructServices, pdbFile, protocol); + pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, + pdbFile, protocol); if (pdb.id != null && pdb.id.trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { @@ -390,15 +395,16 @@ public class StructureSelectionManager for (int s = 0; s < sequence.length; s++) { boolean infChain = true; + final SequenceI seq = sequence[s]; if (targetChains != null && targetChains[s] != null) { infChain = false; targetChain = targetChains[s]; } - else if (sequence[s].getName().indexOf("|") > -1) + else if (seq.getName().indexOf("|") > -1) { - targetChain = sequence[s].getName().substring( - sequence[s].getName().lastIndexOf("|") + 1); + targetChain = seq.getName().substring( + seq.getName().lastIndexOf("|") + 1); if (targetChain.length() > 1) { if (targetChain.trim().length() == 0) @@ -417,14 +423,17 @@ public class StructureSelectionManager targetChain = ""; } + /* + * Attempt pairwise alignment of the sequence with each chain in the PDB, + * and remember the highest scoring chain + */ int max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; boolean first = true; - for (int i = 0; i < pdb.chains.size(); i++) + for (PDBChain chain : pdb.chains) { - PDBChain chain = (pdb.chains.elementAt(i)); if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain) { @@ -432,12 +441,13 @@ public class StructureSelectionManager } // TODO: correctly determine sequence type for mixed na/peptide // structures - AlignSeq as = new AlignSeq(sequence[s], - pdb.chains.elementAt(i).sequence, - pdb.chains.elementAt(i).isNa ? AlignSeq.DNA - : AlignSeq.PEP); - as.calcScoreMatrix(); - as.traceAlignment(); + final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP; + AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence, + type); + // equivalent to: + // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type); + // as.calcScoreMatrix(); + // as.traceAlignment(); if (first || as.maxscore > max || (as.maxscore == max && chain.id.equals(targetChain))) @@ -453,11 +463,13 @@ public class StructureSelectionManager { continue; } - final StringBuffer mappingDetails = new StringBuffer(); - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " - + maxChain.sequence.getSequenceAsString()); - mappingDetails.append("\nNo of residues = " - + maxChain.residues.size() + "\n\n"); + final StringBuilder mappingDetails = new StringBuilder(128); + mappingDetails.append(NEWLINE).append("PDB Sequence is :") + .append(NEWLINE).append("Sequence = ") + .append(maxChain.sequence.getSequenceAsString()); + mappingDetails.append(NEWLINE).append("No of residues = ") + .append(maxChain.residues.size()).append(NEWLINE) + .append(NEWLINE); PrintStream ps = new PrintStream(System.out) { @Override @@ -469,29 +481,34 @@ public class StructureSelectionManager @Override public void println() { - mappingDetails.append("\n"); + mappingDetails.append(NEWLINE); } }; maxAlignseq.printAlignment(ps); - mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start - + " " + maxAlignseq.seq2end); - mappingDetails.append("\nSEQ start/end " - + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " " - + (maxAlignseq.seq1end + sequence[s].getEnd() - 1)); + mappingDetails.append(NEWLINE).append("PDB start/end "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append( + " "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); + + mappingDetails.append(NEWLINE).append("SEQ start/end "); + mappingDetails.append( + String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1)) + .append(" "); + mappingDetails.append(String.valueOf(maxAlignseq.seq1end + + seq.getEnd() - 1)); - maxChain.makeExactMapping(maxAlignseq, sequence[s]); + maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( sqmpping.getMap().getInverse()); - maxChain.transferRESNUMFeatures(sequence[s], null); + maxChain.transferRESNUMFeatures(seq, null); // allocate enough slots to store the mapping from positions in // sequence[s] to the associated chain - int[][] mapping = new int[sequence[s].findPosition(sequence[s] - .getLength()) + 2][2]; + int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; int resNum = -10000; int index = 0; @@ -512,9 +529,8 @@ public class StructureSelectionManager { pdbFile = "INLINE" + pdb.id; } - StructureMapping newMapping = new StructureMapping(sequence[s], - pdbFile, pdb.id, maxChainId, mapping, - mappingDetails.toString()); + StructureMapping newMapping = new StructureMapping(seq, pdbFile, + pdb.id, maxChainId, mapping, mappingDetails.toString()); if (forStructureView) { mappings.add(newMapping); @@ -545,30 +561,30 @@ public class StructureSelectionManager { return; } - String[] handlepdbs; - Vector pdbs = new Vector(); - for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++])) - { - ; - } + + /* + * Remove mappings to the closed listener's PDB files, but first check if + * another listener is still interested + */ + List pdbs = new ArrayList(Arrays.asList(pdbfiles)); + StructureListener sl; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - handlepdbs = sl.getPdbFile(); - for (int j = 0; j < handlepdbs.length; j++) + for (String pdbfile : sl.getPdbFile()) { - if (pdbs.contains(handlepdbs[j])) - { - pdbs.removeElement(handlepdbs[j]); - } + pdbs.remove(pdbfile); } - } } + /* + * Rebuild the mappings set, retaining only those which are for 'other' PDB + * files + */ if (pdbs.size() > 0) { List tmp = new ArrayList(); @@ -846,11 +862,11 @@ public class StructureSelectionManager { List tmp = new ArrayList(); for (StructureMapping sm : mappings) - { + { if (sm.pdbfile.equals(pdbfile)) - { + { tmp.add(sm); - } + } } return tmp.toArray(new StructureMapping[tmp.size()]); } -- 1.7.10.2