X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=dc423158a27a1776209443cd9c9478c074694364;hb=dfa980fc8e8dd186278e5aa1fcf356964afdf61a;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..dc42315 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
@@ -578,6 +598,10 @@ public abstract class AAStructureBindingModel extends
for (String file : files)
{
notLoaded = file;
+ if (file == null)
+ {
+ continue;
+ }
try
{
StructureMapping[] sm = getSsm().getMapping(file);
@@ -613,7 +637,10 @@ 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 +650,14 @@ 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;
+ }
+}