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-3285 small code changes to AnnotationRenderer not included in merge
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
74bec63
..
c6553f8
100644
(file)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-26,6
+26,9
@@
import jalview.appletgui.FeatureRenderer;
import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+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;
@@
-34,8
+37,7
@@
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Color;
import java.awt.Dimension;
-import java.awt.Event;
-import java.awt.Font;
+import java.awt.event.InputEvent;import java.awt.Font;
import java.awt.Graphics;
import java.awt.Image;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
import java.awt.Graphics;
import java.awt.Image;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
@@
-49,8
+51,8
@@
import java.io.PrintStream;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
-public class AppletPDBCanvas extends Panel implements MouseListener,
- MouseMotionListener, StructureListener
+public class AppletPDBCanvas extends Panel
+ implements MouseListener, MouseMotionListener, StructureListener
{
MCMatrix idmat = new MCMatrix(3, 3);
{
MCMatrix idmat = new MCMatrix(3, 3);
@@
-67,7
+69,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
int my = 0;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBEntry pdbentry;
@@
-144,7
+146,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
{
this.ap = ap;
@@
-156,9
+158,9
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
try
{
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setFile("INLINE" + pdb.getId());
}
{
pdbentry.setFile("INLINE" + pdb.getId());
}
@@
-175,7
+177,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
colourBySequence();
colourBySequence();
- int max = -10;
+ float max = -10;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
@@
-189,7
+191,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+ + 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");
@@
-199,16
+202,19
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
pdb.getChains().elementAt(i).sequence,
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
pdb.getChains().elementAt(i).sequence,
- pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+ pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
public void println()
{
mappingDetails.append("\n");
@@
-267,6
+273,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
addKeyListener(new KeyAdapter()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
@@
-470,6
+477,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
centre[2] = ztot / (2 * (float) bsize);
}
centre[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paint(Graphics g)
{
public void paint(Graphics g)
{
@@
-479,9
+487,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(
- MessageManager.getString("label.error_loading_pdb_data"), 50,
- getSize().height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_pdb_data"),
+ 50, getSize().height / 2);
return;
}
return;
}
@@
-569,6
+576,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
showFeatures = true;
}
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
PDBChain chain;
if (bysequence && pdb != null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
@@
-596,25
+605,16
@@
public class AppletPDBCanvas extends Panel 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);
}
}
-
}
}
}
}
}
}
@@
-642,11
+642,15
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
{
tmpBond = visiblebonds.elementAt(i);
{
tmpBond = visiblebonds.elementAt(i);
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
+ xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getSize().height / 2));
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2));
+ xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+ + (getSize().height / 2));
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
@@
-774,6
+778,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
public void mousePressed(MouseEvent e)
{
pdbAction = true;
@@
-818,6
+823,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
dragging = false;
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
@@
-860,18
+866,22
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mouseClicked(MouseEvent e)
{
}
public void mouseClicked(MouseEvent e)
{
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
@@
-882,7
+892,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
MCMatrix objmat = new MCMatrix(3, 3);
objmat.setIdentity();
MCMatrix objmat = new MCMatrix(3, 3);
objmat.setIdentity();
- if ((evt.getModifiers() & Event.META_MASK) != 0)
+ if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
{
objmat.rotatez(((mx - omx)));
}
{
objmat.rotatez(((mx - omx)));
}
@@
-921,6
+931,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
public void mouseReleased(MouseEvent evt)
{
dragging = false;
@@
-956,8
+967,10
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
if (n == 1)
{
if (n == 1)
{
- int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2));
+ int xstart = (int) (((b.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ int ystart = (int) (((centre[1] - b.start[1]) * scale)
+ + (getSize().height / 2));
g.setColor(Color.red);
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
g.setColor(Color.red);
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
@@
-965,8
+978,10
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
if (n == 2)
{
if (n == 2)
{
- int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2));
+ int xstart = (int) (((b.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ int ystart = (int) (((centre[1] - b.end[1]) * scale)
+ + (getSize().height / 2));
g.setColor(Color.red);
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
g.setColor(Color.red);
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
@@
-995,11
+1010,13
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
{
tmpBond = bonds.elementAt(i);
{
tmpBond = bonds.elementAt(i);
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
+ truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
if (Math.abs(truex - x) <= 2)
{
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
+ int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getSize().height / 2));
if (Math.abs(truey - y) <= 2)
{
if (Math.abs(truey - y) <= 2)
{
@@
-1012,11
+1029,13
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// Still here? Maybe its the last bond
// Still here? Maybe its the last bond
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
+ truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
if (Math.abs(truex - x) <= 2)
{
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2));
+ int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+ + (getSize().height / 2));
if (Math.abs(truey - y) <= 2)
{
if (Math.abs(truey - y) <= 2)
{
@@
-1037,6
+1056,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
return fatom;
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
public void update(Graphics g)
{
paint(g);
@@
-1108,7
+1128,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// ////////////////////////////////
// /StructureListener
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ @Override
+ public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}
{
return new String[] { pdbentry.getFile() };
}
@@
-1210,6
+1231,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// return new Color(viewer.getAtomArgb(atomIndex));
}
// return new Color(viewer.getAtomArgb(atomIndex));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
public void updateColours(Object source)
{
colourBySequence();