X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FStructureFile.java;h=7fe17c8d3d6c9bf9a096a98615213ec8cea3d593;hb=6129931bfa23eec90e6556a4d0412ef34aff5759;hp=6ce907ae91f4795faadad23fc03229d46ffaefb6;hpb=6c96743ff6c65895e4b96523d0e3d05f6dc3cb01;p=jalview.git
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 6ce907a..7fe17c8 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;
@@ -22,7 +42,6 @@ import MCview.PDBChain;
public abstract class StructureFile extends AlignFile
{
-
private String id;
private PDBEntry.Type dbRefType;
@@ -47,9 +66,12 @@ public abstract class StructureFile extends AlignFile
private Vector chains;
- public StructureFile(String inFile, String type) throws IOException
+ private boolean pdbIdAvailable;
+
+ public StructureFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public StructureFile(FileParse fp) throws IOException
@@ -76,10 +98,10 @@ public abstract class StructureFile extends AlignFile
}
- public StructureFile(boolean parseImmediately, String dataObject, String type)
- throws IOException
+ public StructureFile(boolean parseImmediately, String dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(parseImmediately, dataObject, type);
+ super(parseImmediately, dataObject, sourceType);
}
public StructureFile(boolean a, FileParse fp) throws IOException
@@ -173,7 +195,7 @@ public abstract class StructureFile extends AlignFile
new Object[] {});
AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
new Class[] { FileParse.class }).invoke(annotate3d,
- new Object[] { new FileParse(getDataName(), type) }));
+ new Object[] { new FileParse(getDataName(), dataSourceType) }));
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
@@ -282,11 +304,8 @@ public abstract class StructureFile extends AlignFile
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl.getConstructor(new Class[] {
- boolean.class, boolean.class, boolean.class, FileParse.class });
- final Object[] args = new Object[] { visibleChainAnnotation,
- predictSecondaryStructure, externalSecondaryStructure,
- new FileParse(getDataName(), type) };
+ final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
@@ -448,4 +467,19 @@ 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;
+ }
}