X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=2ed59aea4b5f7d48d2781867c6f941e257ae2b7b;hb=e77a693cf000b4ff8a863411acf8c90c6390a061;hp=86c9a212c82ae55b996f560e8a39c68f855aebc1;hpb=3bc2fbe640abb0d8941aead117c9624dd16773a3;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 86c9a21..2ed59ae 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -1,9 +1,25 @@ +/* + * 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.StructureSelectionManagerProvider; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; @@ -15,6 +31,10 @@ import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + /** * * A base class to hold common function for protein structure model binding. @@ -52,6 +72,8 @@ public abstract class AAStructureBindingModel extends private boolean nucleotide; + private boolean finishedInit = false; + /** * Data bean class to simplify parameterisation in superposeStructures */ @@ -200,7 +222,9 @@ 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 @@ -208,8 +232,7 @@ 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"); } @@ -218,9 +241,8 @@ public abstract class AAStructureBindingModel extends StringBuilder title = new StringBuilder(64); final PDBEntry pdbEntry = getPdbEntry(0); title.append(viewerName + " view for " + getSequence()[0][0].getName() - + ":" - + pdbEntry.getId()); - + + ":" + pdbEntry.getId()); + if (verbose) { if (pdbEntry.getProperty() != null) @@ -266,8 +288,7 @@ 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 +358,8 @@ 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 +372,7 @@ 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 @@ -601,4 +621,36 @@ public abstract class AAStructureBindingModel extends } return true; } -} \ No newline at end of file + + @Override + public boolean isListeningFor(SequenceI seq) + { + if (sequence != null) + { + for (SequenceI[] seqs : sequence) + { + if (seqs != null) + { + for (SequenceI s : seqs) + { + if (s == seq) + { + return true; + } + } + } + } + } + return false; + } + + public boolean isFinishedInit() + { + return finishedInit; + } + + public void setFinishedInit(boolean fi) + { + this.finishedInit = fi; + } +}