git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2136 merged develop into branch to fix build failure
[jalview.git]
/
src
/
MCview
/
PDBCanvas.java
diff --git
a/src/MCview/PDBCanvas.java
b/src/MCview/PDBCanvas.java
index
1c7a1f7
..
3b12ee9
100644
(file)
--- a/
src/MCview/PDBCanvas.java
+++ b/
src/MCview/PDBCanvas.java
@@
-26,7
+26,9
@@
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
@@
-141,7
+143,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
this.pdbentry = pdbentry;
{
this.ap = ap;
this.pdbentry = pdbentry;
@@
-151,9
+153,10
@@
public class PDBCanvas extends JPanel implements MouseListener,
try
{
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+ ap.alignFrame);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
pdbentry.setFile("INLINE" + pdb.getId());
}
{
pdbentry.setFile("INLINE" + pdb.getId());
}
@@
-188,8
+191,10
@@
public class PDBCanvas extends JPanel implements MouseListener,
for (int i = 0; i < pdb.getChains().size(); i++)
{
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
@@
-543,6
+548,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
showFeatures = true;
}
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
PDBChain chain;
if (bysequence && pdb != null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
@@
-570,23
+576,15
@@
public class PDBCanvas extends JPanel implements MouseListener,
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
- sequence[s], pos);
- }
+ tmp.startCol = sr.getResidueColour(sequence[s], pos,
+ finder);
}
pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
}
pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
- sequence[s], pos);
- }
+ tmp.endCol = sr
+ .getResidueColour(sequence[s], pos, finder);
}
}
}
}
@@
-1078,7
+1076,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
// ////////////////////////////////
// /StructureListener
@Override
// ////////////////////////////////
// /StructureListener
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}
{
return new String[] { pdbentry.getFile() };
}