X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=a34e574b263dfba179cfbf0be476b62bbb1f6cc6;hb=refs%2Fheads%2Ftask%2FJAL-3349_Support_cli_JRE_arguments_through_getdown;hp=0dd58adb3d72ffd6ddfa936eaa3d619958dda17e;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 0dd58ad..a34e574 100644 --- 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.io.DataSourceType; import jalview.io.StructureFile; +import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; @@ -34,8 +36,7 @@ import jalview.structure.StructureSelectionManager; 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.Graphics2D; // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug @@ -53,8 +54,8 @@ import java.util.Vector; 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; @@ -141,7 +142,7 @@ public class PDBCanvas extends JPanel implements MouseListener, String errorMessage; void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap, String protocol) + AlignmentPanel ap, DataSourceType protocol) { this.ap = ap; this.pdbentry = pdbentry; @@ -151,9 +152,10 @@ public class PDBCanvas extends JPanel implements MouseListener, 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()); } @@ -175,7 +177,7 @@ public class PDBCanvas extends JPanel implements MouseListener, colourBySequence(); - int max = -10; + float max = -10; int maxchain = -1; int pdbstart = 0; int pdbend = 0; @@ -188,10 +190,9 @@ public class PDBCanvas extends JPanel implements MouseListener, 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"); @@ -545,6 +546,7 @@ public class PDBCanvas extends JPanel implements MouseListener, showFeatures = true; } + FeatureColourFinder finder = new FeatureColourFinder(fr); PDBChain chain; if (bysequence && pdb != null) { @@ -572,23 +574,15 @@ public class PDBCanvas extends JPanel implements MouseListener, 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); - 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); } } @@ -618,11 +612,15 @@ public class PDBCanvas extends JPanel implements MouseListener, { 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; @@ -686,8 +684,8 @@ public class PDBCanvas extends JPanel implements MouseListener, 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); } @@ -823,8 +821,8 @@ public class PDBCanvas extends JPanel implements MouseListener, if (fatom != null) { - this.setToolTipText(chain.id + ":" + fatom.resNumber + " " - + fatom.resName); + this.setToolTipText( + chain.id + ":" + fatom.resNumber + " " + fatom.resName); } else { @@ -859,7 +857,7 @@ public class PDBCanvas extends JPanel implements MouseListener, 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))); } @@ -934,16 +932,20 @@ public class PDBCanvas extends JPanel implements MouseListener, 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) { - 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); } @@ -969,11 +971,13 @@ public class PDBCanvas extends JPanel implements MouseListener, { 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) { - 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) { @@ -986,11 +990,13 @@ public class PDBCanvas extends JPanel implements MouseListener, // 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) { - 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) { @@ -1080,7 +1086,7 @@ public class PDBCanvas extends JPanel implements MouseListener, // //////////////////////////////// // /StructureListener @Override - public String[] getPdbFile() + public String[] getStructureFiles() { return new String[] { pdbentry.getFile() }; }