/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.io.*;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Event;
+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.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-import jalview.appletgui.*;
-import jalview.structure.*;
-import jalview.util.MessageManager;
+import java.awt.Panel;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.io.PrintStream;
+import java.util.List;
+import java.util.Vector;
public class AppletPDBCanvas extends Panel implements MouseListener,
MouseMotionListener, StructureListener
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBChain mainchain;
- Vector highlightRes;
+ Vector<String> highlightRes;
boolean pdbAction = false;
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbentry.setFile("INLINE" + pdb.id);
+ {
+ pdbentry.setFile("INLINE" + pdb.getId());
+ }
} catch (Exception ex)
{
return;
}
- pdbentry.setId(pdb.id);
+ pdbentry.setId(pdb.getId());
ssm.addStructureViewerListener(this);
// JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + ((PDBChain) pdb.chains.elementAt(i)).sequence
- .getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
- + "\n\n");
+ + pdb.getChains().elementAt(i).residues.size() + "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
- ((PDBChain) pdb.chains.elementAt(i)).sequence,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
+ pdb.getChains().elementAt(i).sequence, pdb.getChains()
+ .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
- mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+ mainchain = pdb.getChains().elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
scale = findScale();
}
- Vector visiblebonds;
+ Vector<Bond> visiblebonds;
void setupBonds()
{
seqColoursReady = false;
// Sort the bonds by z coord
- visiblebonds = new Vector();
+ visiblebonds = new Vector<Bond>();
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
for (int i = 0; i < tmp.size(); i++)
{
min[1] = (float) 1e30;
min[2] = (float) 1e30;
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond tmp : bonds)
{
- Bond tmp = (Bond) bonds.elementAt(i);
-
if (tmp.start[0] >= max[0])
{
max[0] = tmp.start[0];
}
}
- width[0] = (float) Math.abs(max[0] - min[0]);
- width[1] = (float) Math.abs(max[1] - min[1]);
- width[2] = (float) Math.abs(max[2] - min[2]);
+ width[0] = Math.abs(max[0] - min[0]);
+ width[1] = Math.abs(max[1] - min[1]);
+ width[2] = Math.abs(max[2] - min[2]);
maxwidth = width[0];
int bsize = 0;
// Find centre coordinate
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ if (pdb.getChains().elementAt(ii).isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
bsize += bonds.size();
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- xtot = xtot + ((Bond) bonds.elementAt(i)).start[0]
- + ((Bond) bonds.elementAt(i)).end[0];
-
- ytot = ytot + ((Bond) bonds.elementAt(i)).start[1]
- + ((Bond) bonds.elementAt(i)).end[1];
-
- ztot = ztot + ((Bond) bonds.elementAt(i)).start[2]
- + ((Bond) bonds.elementAt(i)).end[2];
+ xtot = xtot + b.start[0] + b.end[0];
+ ytot = ytot + b.start[1] + b.end[1];
+ ztot = ztot + b.start[2] + b.end[2];
}
}
}
centre[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paint(Graphics g)
{
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;
}
{
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
+ getSize().height / 2);
return;
}
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
- if (ap.av.getShowSequenceFeatures())
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- chain = (PDBChain) pdb.chains.elementAt(ii);
+ chain = pdb.getChains().elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
- Bond tmp = (Bond) chain.bonds.elementAt(i);
+ Bond tmp = chain.bonds.elementAt(i);
tmp.startCol = Color.lightGray;
tmp.endCol = Color.lightGray;
if (chain != mainchain)
zsort = new Zsort();
}
- zsort.Zsort(visiblebonds);
+ zsort.sort(visiblebonds);
}
Bond tmpBond = null;
for (int i = 0; i < visiblebonds.size(); i++)
{
- tmpBond = (Bond) 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));
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
repaint();
if (foundchain != -1)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ PDBChain chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
{
if (highlightRes == null)
{
- highlightRes = new Vector();
+ highlightRes = new Vector<String>();
}
- if (highlightRes.contains(fatom.alignmentMapping + "" + ""))
+ final String atomString = Integer
+ .toString(fatom.alignmentMapping);
+ if (highlightRes.contains(atomString))
{
- highlightRes.removeElement(fatom.alignmentMapping + "");
+ highlightRes.removeElement(atomString);
}
else
{
- highlightRes.addElement(fatom.alignmentMapping + "");
+ highlightRes.addElement(atomString);
}
}
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
PDBChain chain = null;
if (foundchain != -1)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
}
}
+ @Override
public void mouseClicked(MouseEvent e)
{
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
if ((evt.getModifiers() & Event.META_MASK) != 0)
{
- objmat.rotatez((float) ((mx - omx)));
+ objmat.rotatez(((mx - omx)));
}
else
{
- objmat.rotatex((float) ((omy - my)));
- objmat.rotatey((float) ((omx - mx)));
+ objmat.rotatex(((omy - my)));
+ objmat.rotatey(((omx - mx)));
}
// Alter the bonds
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (PDBChain chain : pdb.getChains())
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond tmpBond : chain.bonds)
{
- Bond tmpBond = (Bond) bonds.elementAt(i);
-
// Translate the bond so the centre is 0,0,0
tmpBond.translate(-centre[0], -centre[1], -centre[2]);
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
void drawLabels(Graphics g)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (PDBChain chain : pdb.getChains())
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
-
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond tmpBond : chain.bonds)
{
- Bond tmpBond = (Bond) bonds.elementAt(i);
-
if (tmpBond.at1.isSelected)
{
labelAtom(g, tmpBond, 1);
if (tmpBond.at2.isSelected)
{
-
labelAtom(g, tmpBond, 2);
}
}
foundchain = -1;
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
- Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+ Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
for (int i = 0; i < bonds.size(); i++)
{
- tmpBond = (Bond) bonds.elementAt(i);
+ tmpBond = bonds.elementAt(i);
truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
if (fatom != null) // )&& chain.ds != null)
{
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
}
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
{
- tmpBond = (Bond) mainchain.bonds.elementAt(index);
+ tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.alignmentMapping == ii - 1)
{
if (highlightBond1 != null)
if (index > 0)
{
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
public void setAllchainsVisible(boolean b)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
// ////////////////////////////////
// /StructureListener
+ @Override
public String[] getPdbFile()
{
- return new String[]
- { pdbentry.getFile() };
+ return new String[] { pdbentry.getFile() };
}
String lastMessage;
public void mouseOverStructure(int pdbResNum, String chain)
{
if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+ {
ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+ }
lastMessage = pdbResNum + chain;
}
StringBuffer eval = new StringBuffer();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ /**
+ * Highlight the specified atoms in the structure.
+ *
+ * @param atoms
+ */
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
{
if (!seqColoursReady)
{
return;
}
-
- if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
+ for (AtomSpec atom : atoms)
{
- return;
+ int atomIndex = atom.getAtomIndex();
+
+ if (highlightRes != null
+ && highlightRes.contains((atomIndex - 1) + ""))
+ {
+ continue;
+ }
+
+ highlightAtom(atomIndex);
}
+ redrawneeded = true;
+ repaint();
+ }
+
+ /**
+ * @param atomIndex
+ */
+ protected void highlightAtom(int atomIndex)
+ {
int index = -1;
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
{
- tmpBond = (Bond) mainchain.bonds.elementAt(index);
+ tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.atomIndex == atomIndex)
{
if (highlightBond1 != null)
if (index > 0)
{
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
break;
}
}
-
- redrawneeded = true;
- repaint();
}
public Color getColour(int atomIndex, int pdbResNum, String chain,
// return new Color(viewer.getAtomArgb(atomIndex));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
}
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI s : sequence)
+ {
+ if (s == seq)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff