/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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 jalview.ext.jmol;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import java.awt.Color;
import java.util.ArrayList;
+import java.util.List;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding another
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
-
- ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ ColumnSelection cs = viewport.getColumnSelection();
+ AlignmentI al = viewport.getAlignment();
+ List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
ArrayList<String> str = new ArrayList<String>();
if (mapping == null || mapping.length < 1)
+ {
continue;
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
for (int sp, m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
+
+ /*
+ * shade hidden regions darker
+ */
+ if (!cs.isVisible(r))
+ {
+ col = Color.GRAY;
+ }
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
command.append("select " + pos);
command.append(newSelcom);
}
- break;
+ // break;
}
}
}