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JAL-2719 JAL-1264 add annotation elements so “Add Reference Annotation” menu should...
[jalview.git]
/
src
/
MCview
/
PDBCanvas.java
diff --git
a/src/MCview/PDBCanvas.java
b/src/MCview/PDBCanvas.java
index
dfe7c8f
..
ab172f2
100644
(file)
--- a/
src/MCview/PDBCanvas.java
+++ b/
src/MCview/PDBCanvas.java
@@
-26,6
+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.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;
@@
-52,8
+55,8
@@
import java.util.Vector;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
-public class PDBCanvas extends JPanel implements MouseListener,
- MouseMotionListener, StructureListener
+public class PDBCanvas extends JPanel
+ implements MouseListener, MouseMotionListener, StructureListener
{
boolean redrawneeded = true;
{
boolean redrawneeded = true;
@@
-65,7
+68,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
int my = 0;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBEntry pdbentry;
@@
-140,7
+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;
@@
-150,9
+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());
}
@@
-174,7
+178,7
@@
public class PDBCanvas extends JPanel 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;
@@
-188,7
+192,8
@@
public class PDBCanvas extends JPanel 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");
@@
-201,11
+206,13
@@
public class PDBCanvas extends JPanel implements MouseListener,
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
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");
@@
-245,6
+252,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
addKeyListener(new KeyAdapter()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
keyPressed(evt);
public void keyPressed(KeyEvent evt)
{
keyPressed(evt);
@@
-452,6
+460,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
centre[2] = ztot / (2 * (float) bsize);
}
centre[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
public void paintComponent(Graphics g)
{
super.paintComponent(g);
@@
-538,6
+547,7
@@
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)
{
@@
-565,23
+575,15
@@
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);
}
}
}
}
@@
-611,11
+613,15
@@
public class PDBCanvas extends JPanel implements MouseListener,
{
tmpBond = visiblebonds.elementAt(i);
{
tmpBond = visiblebonds.elementAt(i);
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+ xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getHeight() / 2));
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getHeight() / 2));
+ xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+ + (getHeight() / 2));
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
@@
-679,8
+685,8
@@
public class PDBCanvas extends JPanel implements MouseListener,
if (highlightBond1 != null && highlightBond1 == tmpBond)
{
if (highlightBond1 != null && highlightBond1 == tmpBond)
{
- g.setColor(tmpBond.endCol.brighter().brighter().brighter()
- .brighter());
+ g.setColor(
+ tmpBond.endCol.brighter().brighter().brighter().brighter());
drawLine(g, xmid, ymid, xend, yend);
}
drawLine(g, xmid, ymid, xend, yend);
}
@@
-745,6
+751,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
public void mousePressed(MouseEvent e)
{
pdbAction = true;
@@
-789,6
+796,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
dragging = false;
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
@@
-814,8
+822,8
@@
public class PDBCanvas extends JPanel implements MouseListener,
if (fatom != null)
{
if (fatom != null)
{
- this.setToolTipText(chain.id + ":" + fatom.resNumber + " "
- + fatom.resName);
+ this.setToolTipText(
+ chain.id + ":" + fatom.resNumber + " " + fatom.resName);
}
else
{
}
else
{
@@
-824,18
+832,22
@@
public class PDBCanvas extends JPanel 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();
@@
-885,6
+897,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
public void mouseReleased(MouseEvent evt)
{
dragging = false;
@@
-920,16
+933,20
@@
public class PDBCanvas extends JPanel implements MouseListener,
g.setColor(Color.red);
if (n == 1)
{
g.setColor(Color.red);
if (n == 1)
{
- int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getHeight() / 2));
+ int xstart = (int) (((b.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ int ystart = (int) (((centre[1] - b.start[1]) * scale)
+ + (getHeight() / 2));
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
}
if (n == 2)
{
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
}
if (n == 2)
{
- int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getHeight() / 2));
+ int xstart = (int) (((b.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ int ystart = (int) (((centre[1] - b.end[1]) * scale)
+ + (getHeight() / 2));
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
}
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
}
@@
-955,11
+972,13
@@
public class PDBCanvas extends JPanel implements MouseListener,
{
tmpBond = bond;
{
tmpBond = bond;
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
+ truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+ int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
if (Math.abs(truey - y) <= 2)
{
@@
-972,11
+991,13
@@
public class PDBCanvas extends JPanel implements MouseListener,
// Still here? Maybe its the last bond
// Still here? Maybe its the last bond
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
+ truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getHeight() / 2));
+ int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+ + (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
if (Math.abs(truey - y) <= 2)
{
@@
-1065,7
+1086,8
@@
public class PDBCanvas extends JPanel implements MouseListener,
// ////////////////////////////////
// /StructureListener
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ @Override
+ public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}
{
return new String[] { pdbentry.getFile() };
}
@@
-1169,6
+1191,7
@@
public class PDBCanvas extends JPanel 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();