-/*
- * 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.
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.analysis.NJTree;
-import jalview.api.AlignViewportI;
-import jalview.bin.JalviewLite;
-import jalview.commands.CommandI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.AlignCalcManager;
-
-import java.awt.Font;
-
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource, VamsasSource, CommandListener
-{
- boolean cursorMode = false;
-
- Font font = new Font("SansSerif", Font.PLAIN, 10);
-
- boolean validCharWidth = true;
-
- NJTree currentTree = null;
-
- public JalviewLite applet;
-
- boolean MAC = false;
-
- private AnnotationColumnChooser annotationColumnSelectionState;
-
- public void finalize()
- {
- applet = null;
- quality = null;
- alignment = null;
- colSel = null;
- }
-
- public AlignViewport(AlignmentI al, JalviewLite applet)
- {
- super();
- calculator = new AlignCalcManager();
- this.applet = applet;
- alignment = al;
- // we always pad gaps
- this.setPadGaps(true);
- this.startRes = 0;
- this.endRes = al.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = al.getHeight() - 1;
- if (applet != null)
- {
- // get the width and height scaling factors if they were specified
- String param = applet.getParameter("widthScale");
- if (param != null)
- {
- try
- {
- widthScale = new Float(param).floatValue();
- } catch (Exception e)
- {
- }
- if (widthScale <= 1.0)
- {
- System.err
- .println("Invalid alignment character width scaling factor ("
- + widthScale + "). Ignoring.");
- widthScale = 1;
- }
- if (JalviewLite.debug)
- {
- System.err
- .println("Alignment character width scaling factor is now "
- + widthScale);
- }
- }
- param = applet.getParameter("heightScale");
- if (param != null)
- {
- try
- {
- heightScale = new Float(param).floatValue();
- } catch (Exception e)
- {
- }
- if (heightScale <= 1.0)
- {
- System.err
- .println("Invalid alignment character height scaling factor ("
- + heightScale + "). Ignoring.");
- heightScale = 1;
- }
- if (JalviewLite.debug)
- {
- System.err
- .println("Alignment character height scaling factor is now "
- + heightScale);
- }
- }
- }
- setFont(font);
-
- MAC = Platform.isAMac();
-
- if (applet != null)
- {
- setShowJVSuffix(applet.getDefaultParameter("showFullId",
- getShowJVSuffix()));
-
- setShowAnnotation(applet.getDefaultParameter("showAnnotation",
- isShowAnnotation()));
-
- showConservation = applet.getDefaultParameter("showConservation",
- showConservation);
-
- showQuality = applet.getDefaultParameter("showQuality", showQuality);
-
- showConsensus = applet.getDefaultParameter("showConsensus",
- showConsensus);
-
- setShowUnconserved(applet.getDefaultParameter("showUnconserved",
- getShowUnconserved()));
-
- setScaleProteinAsCdna(applet.getDefaultParameter(
- "scaleProteinAsCdna", isScaleProteinAsCdna()));
-
- String param = applet.getParameter("upperCase");
- if (param != null)
- {
- if (param.equalsIgnoreCase("bold"))
- {
- setUpperCasebold(true);
- }
- }
- sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
-
- setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
- isFollowHighlight()));
- followSelection = isFollowHighlight();
-
- showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
- showSequenceLogo);
-
- normaliseSequenceLogo = applet.getDefaultParameter(
- "normaliseSequenceLogo", applet.getDefaultParameter(
- "normaliseLogo", normaliseSequenceLogo));
-
- showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
- showGroupConsensus);
-
- showGroupConservation = applet.getDefaultParameter(
- "showGroupConservation", showGroupConservation);
-
- showConsensusHistogram = applet.getDefaultParameter(
- "showConsensusHistogram", showConsensusHistogram);
-
- }
-
- if (applet != null)
- {
- String colour = applet.getParameter("defaultColour");
-
- if (colour == null)
- {
- colour = applet.getParameter("userDefinedColour");
- if (colour != null)
- {
- colour = "User Defined";
- }
- }
-
- if (colour != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- colour);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
-
- if (applet.getParameter("userDefinedColour") != null)
- {
- ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
- .getParameter("userDefinedColour"));
- }
- }
- initAutoAnnotation();
-
- }
-
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)
- {
- updateConsensus(null);
- }
- if (consensus == null)
- {
- return null;
- }
- StringBuilder seqs = new StringBuilder(consensus.annotations.length);
- for (int i = 0; i < consensus.annotations.length; i++)
- {
- if (consensus.annotations[i] != null)
- {
- if (consensus.annotations[i].description.charAt(0) == '[')
- {
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
- {
- seqs.append(consensus.annotations[i].displayCharacter);
- }
- }
- }
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
- }
-
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- private float heightScale = 1, widthScale = 1;
-
- public void setFont(Font f)
- {
- font = f;
- if (nullFrame == null)
- {
- nullFrame = new java.awt.Frame();
- nullFrame.addNotify();
- }
-
- java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight((int) (heightScale * fm.getHeight()));
- setCharWidth((int) (widthScale * fm.charWidth('M')));
-
- if (isUpperCasebold())
- {
- Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
- fm = nullFrame.getGraphics().getFontMetrics(f2);
- setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
- }
- }
-
- public Font getFont()
- {
- return font;
- }
-
-
- public void resetSeqLimits(int height)
- {
- setEndSeq(height / getCharHeight());
- }
-
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
-
- boolean centreColumnLabels;
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public boolean followSelection = true;
-
- /**
- * @return true if view selection should always follow the selections
- * broadcast by other selection sources
- */
- public boolean getFollowSelection()
- {
- return followSelection;
- }
-
- public void sendSelection()
- {
- getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
- }
-
- /**
- * Returns an instance of the StructureSelectionManager scoped to this applet
- * instance.
- *
- * @return
- */
- @Override
- public StructureSelectionManager getStructureSelectionManager()
- {
- return StructureSelectionManager.getStructureSelectionManager(applet);
- }
-
- /**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
- *
- * @param sg
- * @param wholewidth
- */
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
- {
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
- {
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
- }
- }
-
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
- /**
- *
- * @return true if alignment characters should be displayed
- */
- public boolean isValidCharWidth()
- {
- return validCharWidth;
- }
-
- public AnnotationColumnChooser getAnnotationColumnSelectionState()
- {
- return annotationColumnSelectionState;
- }
-
- public void setAnnotationColumnSelectionState(
- AnnotationColumnChooser annotationColumnSelectionState)
- {
- this.annotationColumnSelectionState = annotationColumnSelectionState;
- }
-
- @Override
- public void mirrorCommand(CommandI command, boolean undo,
- StructureSelectionManager ssm, VamsasSource source)
- {
- // TODO refactor so this can be pulled up to superclass or controller
- /*
- * Do nothing unless we are a 'complement' of the source. May replace this
- * with direct calls not via SSM.
- */
- if (source instanceof AlignViewportI
- && ((AlignViewportI) source).getCodingComplement() == this)
- {
- // ok to continue;
- }
- else
- {
- return;
- }
-
- CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
- getGapCharacter());
- if (mappedCommand != null)
- {
- mappedCommand.doCommand(null);
- firePropertyChange("alignment", null, getAlignment().getSequences());
-
- // ap.scalePanelHolder.repaint();
- // ap.repaint();
- }
- }
-
- @Override
- public VamsasSource getVamsasSource()
- {
- return this;
- }
-
- /**
- * If this viewport has a (Protein/cDNA) complement, then scroll the
- * complementary alignment to match this one.
- */
- public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
- {
- if (complementPanel == null)
- {
- return;
- }
-
- /*
- * Populate a SearchResults object with the mapped location to scroll to. If
- * there is no complement, or it is not following highlights, or no mapping
- * is found, the result will be empty.
- */
- SearchResults sr = new SearchResults();
- int seqOffset = findComplementScrollTarget(sr);
- if (!sr.isEmpty())
- {
- complementPanel.setFollowingComplementScroll(true);
- complementPanel.scrollToCentre(sr, seqOffset);
- }
- }
-
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.NJTree;\r
+import jalview.api.AlignViewportI;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.CommandI;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.schemes.ColourSchemeProperty;\r
+import jalview.schemes.UserColourScheme;\r
+import jalview.structure.CommandListener;\r
+import jalview.structure.SelectionSource;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.structure.VamsasSource;\r
+import jalview.util.Platform;\r
+import jalview.viewmodel.AlignmentViewport;\r
+import jalview.workers.AlignCalcManager;\r
+\r
+import java.awt.Font;\r
+\r
+public class AlignViewport extends AlignmentViewport implements\r
+ SelectionSource, VamsasSource, CommandListener\r
+{\r
+ boolean cursorMode = false;\r
+\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+\r
+ boolean validCharWidth = true;\r
+\r
+ NJTree currentTree = null;\r
+\r
+ public JalviewLite applet;\r
+\r
+ boolean MAC = false;\r
+\r
+ private AnnotationColumnChooser annotationColumnSelectionState;\r
+\r
+ public void finalize()\r
+ {\r
+ applet = null;\r
+ quality = null;\r
+ alignment = null;\r
+ colSel = null;\r
+ }\r
+\r
+ public AlignViewport(AlignmentI al, JalviewLite applet)\r
+ {\r
+ super();\r
+ calculator = new AlignCalcManager();\r
+ this.applet = applet;\r
+ alignment = al;\r
+ // we always pad gaps\r
+ this.setPadGaps(true);\r
+ this.startRes = 0;\r
+ this.endRes = al.getWidth() - 1;\r
+ this.startSeq = 0;\r
+ this.endSeq = al.getHeight() - 1;\r
+ if (applet != null)\r
+ {\r
+ // get the width and height scaling factors if they were specified\r
+ String param = applet.getParameter("widthScale");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ widthScale = new Float(param).floatValue();\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ if (widthScale <= 1.0)\r
+ {\r
+ System.err\r
+ .println("Invalid alignment character width scaling factor ("\r
+ + widthScale + "). Ignoring.");\r
+ widthScale = 1;\r
+ }\r
+ if (JalviewLite.debug)\r
+ {\r
+ System.err\r
+ .println("Alignment character width scaling factor is now "\r
+ + widthScale);\r
+ }\r
+ }\r
+ param = applet.getParameter("heightScale");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ heightScale = new Float(param).floatValue();\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ if (heightScale <= 1.0)\r
+ {\r
+ System.err\r
+ .println("Invalid alignment character height scaling factor ("\r
+ + heightScale + "). Ignoring.");\r
+ heightScale = 1;\r
+ }\r
+ if (JalviewLite.debug)\r
+ {\r
+ System.err\r
+ .println("Alignment character height scaling factor is now "\r
+ + heightScale);\r
+ }\r
+ }\r
+ }\r
+ setFont(font);\r
+\r
+ MAC = Platform.isAMac();\r
+\r
+ if (applet != null)\r
+ {\r
+ setShowJVSuffix(applet.getDefaultParameter("showFullId",\r
+ getShowJVSuffix()));\r
+\r
+ setShowAnnotation(applet.getDefaultParameter("showAnnotation",\r
+ isShowAnnotation()));\r
+\r
+ showConservation = applet.getDefaultParameter("showConservation",\r
+ showConservation);\r
+\r
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);\r
+\r
+ showConsensus = applet.getDefaultParameter("showConsensus",\r
+ showConsensus);\r
+\r
+ setShowUnconserved(applet.getDefaultParameter("showUnconserved",\r
+ getShowUnconserved()));\r
+\r
+ setScaleProteinAsCdna(applet.getDefaultParameter(\r
+ "scaleProteinAsCdna", isScaleProteinAsCdna()));\r
+\r
+ String param = applet.getParameter("upperCase");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("bold"))\r
+ {\r
+ setUpperCasebold(true);\r
+ }\r
+ }\r
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);\r
+\r
+ setFollowHighlight(applet.getDefaultParameter("automaticScrolling",\r
+ isFollowHighlight()));\r
+ followSelection = isFollowHighlight();\r
+\r
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",\r
+ showSequenceLogo);\r
+\r
+ normaliseSequenceLogo = applet.getDefaultParameter(\r
+ "normaliseSequenceLogo", applet.getDefaultParameter(\r
+ "normaliseLogo", normaliseSequenceLogo));\r
+\r
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",\r
+ showGroupConsensus);\r
+\r
+ showGroupConservation = applet.getDefaultParameter(\r
+ "showGroupConservation", showGroupConservation);\r
+\r
+ showConsensusHistogram = applet.getDefaultParameter(\r
+ "showConsensusHistogram", showConsensusHistogram);\r
+\r
+ }\r
+\r
+ if (applet != null)\r
+ {\r
+ String colour = applet.getParameter("defaultColour");\r
+\r
+ if (colour == null)\r
+ {\r
+ colour = applet.getParameter("userDefinedColour");\r
+ if (colour != null)\r
+ {\r
+ colour = "User Defined";\r
+ }\r
+ }\r
+\r
+ if (colour != null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
+ colour);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(hconsensus);\r
+ }\r
+ }\r
+\r
+ if (applet.getParameter("userDefinedColour") != null)\r
+ {\r
+ ((UserColourScheme) globalColourScheme).parseAppletParameter(applet\r
+ .getParameter("userDefinedColour"));\r
+ }\r
+ }\r
+ initAutoAnnotation();\r
+\r
+ }\r
+\r
+ /**\r
+ * get the consensus sequence as displayed under the PID consensus annotation\r
+ * row.\r
+ * \r
+ * @return consensus sequence as a new sequence object\r
+ */\r
+ public SequenceI getConsensusSeq()\r
+ {\r
+ if (consensus == null)\r
+ {\r
+ updateConsensus(null);\r
+ }\r
+ if (consensus == null)\r
+ {\r
+ return null;\r
+ }\r
+ StringBuilder seqs = new StringBuilder(consensus.annotations.length);\r
+ for (int i = 0; i < consensus.annotations.length; i++)\r
+ {\r
+ if (consensus.annotations[i] != null)\r
+ {\r
+ if (consensus.annotations[i].description.charAt(0) == '[')\r
+ {\r
+ seqs.append(consensus.annotations[i].description.charAt(1));\r
+ }\r
+ else\r
+ {\r
+ seqs.append(consensus.annotations[i].displayCharacter);\r
+ }\r
+ }\r
+ }\r
+ SequenceI sq = new Sequence("Consensus", seqs.toString());\r
+ sq.setDescription("Percentage Identity Consensus "\r
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));\r
+ return sq;\r
+ }\r
+\r
+ java.awt.Frame nullFrame;\r
+\r
+ protected FeatureSettings featureSettings = null;\r
+\r
+ private float heightScale = 1, widthScale = 1;\r
+\r
+ public void setFont(Font f)\r
+ {\r
+ font = f;\r
+ if (nullFrame == null)\r
+ {\r
+ nullFrame = new java.awt.Frame();\r
+ nullFrame.addNotify();\r
+ }\r
+\r
+ java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);\r
+ setCharHeight((int) (heightScale * fm.getHeight()));\r
+ setCharWidth((int) (widthScale * fm.charWidth('M')));\r
+\r
+ if (isUpperCasebold())\r
+ {\r
+ Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());\r
+ fm = nullFrame.getGraphics().getFontMetrics(f2);\r
+ setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));\r
+ }\r
+ }\r
+\r
+ public Font getFont()\r
+ {\r
+ return font;\r
+ }\r
+\r
+\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
+ }\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
+ }\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
+ return currentTree;\r
+ }\r
+\r
+\r
+ boolean centreColumnLabels;\r
+\r
+ public boolean getCentreColumnLabels()\r
+ {\r
+ return centreColumnLabels;\r
+ }\r
+\r
+ public boolean followSelection = true;\r
+\r
+ /**\r
+ * @return true if view selection should always follow the selections\r
+ * broadcast by other selection sources\r
+ */\r
+ public boolean getFollowSelection()\r
+ {\r
+ return followSelection;\r
+ }\r
+\r
+ public void sendSelection()\r
+ {\r
+ getStructureSelectionManager().sendSelection(\r
+ new SequenceGroup(getSelectionGroup()),\r
+ new ColumnSelection(getColumnSelection()), this);\r
+ }\r
+\r
+ /**\r
+ * Returns an instance of the StructureSelectionManager scoped to this applet\r
+ * instance.\r
+ * \r
+ * @return\r
+ */\r
+ @Override\r
+ public StructureSelectionManager getStructureSelectionManager()\r
+ {\r
+ return StructureSelectionManager.getStructureSelectionManager(applet);\r
+ }\r
+\r
+ /**\r
+ * synthesize a column selection if none exists so it covers the given\r
+ * selection group. if wholewidth is false, no column selection is made if the\r
+ * selection group covers the whole alignment width.\r
+ * \r
+ * @param sg\r
+ * @param wholewidth\r
+ */\r
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)\r
+ {\r
+ int sgs, sge;\r
+ if (sg != null\r
+ && (sgs = sg.getStartRes()) >= 0\r
+ && sg.getStartRes() <= (sge = sg.getEndRes())\r
+ && (colSel == null || colSel.getSelected() == null || colSel\r
+ .getSelected().size() == 0))\r
+ {\r
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))\r
+ {\r
+ // do nothing\r
+ return;\r
+ }\r
+ if (colSel == null)\r
+ {\r
+ colSel = new ColumnSelection();\r
+ }\r
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)\r
+ {\r
+ colSel.addElement(cspos);\r
+ }\r
+ }\r
+ }\r
+\r
+ public boolean isNormaliseSequenceLogo()\r
+ {\r
+ return normaliseSequenceLogo;\r
+ }\r
+\r
+ public void setNormaliseSequenceLogo(boolean state)\r
+ {\r
+ normaliseSequenceLogo = state;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return true if alignment characters should be displayed\r
+ */\r
+ public boolean isValidCharWidth()\r
+ {\r
+ return validCharWidth;\r
+ }\r
+\r
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()\r
+ {\r
+ return annotationColumnSelectionState;\r
+ }\r
+\r
+ public void setAnnotationColumnSelectionState(\r
+ AnnotationColumnChooser annotationColumnSelectionState)\r
+ {\r
+ this.annotationColumnSelectionState = annotationColumnSelectionState;\r
+ }\r
+\r
+ @Override\r
+ public void mirrorCommand(CommandI command, boolean undo,\r
+ StructureSelectionManager ssm, VamsasSource source)\r
+ {\r
+ // TODO refactor so this can be pulled up to superclass or controller\r
+ /*\r
+ * Do nothing unless we are a 'complement' of the source. May replace this\r
+ * with direct calls not via SSM.\r
+ */\r
+ if (source instanceof AlignViewportI\r
+ && ((AlignViewportI) source).getCodingComplement() == this)\r
+ {\r
+ // ok to continue;\r
+ }\r
+ else\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),\r
+ getGapCharacter());\r
+ if (mappedCommand != null)\r
+ {\r
+ mappedCommand.doCommand(null);\r
+ firePropertyChange("alignment", null, getAlignment().getSequences());\r
+\r
+ // ap.scalePanelHolder.repaint();\r
+ // ap.repaint();\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public VamsasSource getVamsasSource()\r
+ {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * If this viewport has a (Protein/cDNA) complement, then scroll the\r
+ * complementary alignment to match this one.\r
+ */\r
+ public void scrollComplementaryAlignment(AlignmentPanel complementPanel)\r
+ {\r
+ if (complementPanel == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ /*\r
+ * Populate a SearchResults object with the mapped location to scroll to. If\r
+ * there is no complement, or it is not following highlights, or no mapping\r
+ * is found, the result will be empty.\r
+ */\r
+ SearchResults sr = new SearchResults();\r
+ int seqOffset = findComplementScrollTarget(sr);\r
+ if (!sr.isEmpty())\r
+ {\r
+ complementPanel.setFollowingComplementScroll(true);\r
+ complementPanel.scrollToCentre(sr, seqOffset);\r
+ }\r
+ }\r
+\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff