X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStructureFile.java;h=26c202c91c941e996d89e75a7c838cbc0620e7fa;hb=d7361eaa08dc9af7d996851f39b7a2007d1b8832;hp=0bc6a73f40c5ebeb40b192b02a430f75fdbd156c;hpb=ce6f02a53c98e51cb96533d40db5f94d1bfea00a;p=jalview.git
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 0bc6a73..26c202c 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,3 +1,23 @@
+/*
+ * 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.io;
import jalview.analysis.AlignSeq;
@@ -15,7 +35,6 @@ import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.io.IOException;
import java.lang.reflect.Constructor;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
@@ -48,6 +67,8 @@ public abstract class StructureFile extends AlignFile
private Vector chains;
+ private boolean pdbIdAvailable;
+
public StructureFile(String inFile, String type) throws IOException
{
super(inFile, type);
@@ -77,8 +98,8 @@ public abstract class StructureFile extends AlignFile
}
- public StructureFile(boolean parseImmediately, String dataObject, String type)
- throws IOException
+ public StructureFile(boolean parseImmediately, String dataObject,
+ String type) throws IOException
{
super(parseImmediately, dataObject, type);
}
@@ -92,7 +113,6 @@ public abstract class StructureFile extends AlignFile
{
}
- @SuppressWarnings("rawtypes")
protected SequenceI postProcessChain(PDBChain chain)
{
SequenceI pdbSequence = chain.sequence;
@@ -100,10 +120,9 @@ public abstract class StructureFile extends AlignFile
PDBEntry entry = new PDBEntry();
entry.setId(getId());
entry.setType(getStructureFileType());
- entry.setProperty(new Hashtable());
if (chain.id != null)
{
- entry.setChainCode(String.valueOf(chain.id));
+ entry.setChainCode(chain.id);
}
if (inFile != null)
{
@@ -450,4 +469,19 @@ public abstract class StructureFile extends AlignFile
{
return new PDBFeatureSettings();
}
+
+ /**
+ * Answers true if the structure file has a PDBId
+ *
+ * @return
+ */
+ public boolean isPPDBIdAvailable()
+ {
+ return pdbIdAvailable;
+ }
+
+ public void setPDBIdAvailable(boolean pdbIdAvailable)
+ {
+ this.pdbIdAvailable = pdbIdAvailable;
+ }
}