/*
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.api.AlignViewportI;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Font;
import java.awt.FontMetrics;
public class AlignViewport extends AlignmentViewport
implements SelectionSource
{
boolean cursorMode = false;
Font font = new Font("SansSerif", Font.PLAIN, 10);
boolean validCharWidth = true;
public jalview.bin.JalviewLite applet;
private AnnotationColumnChooser annotationColumnSelectionState;
java.awt.Frame nullFrame;
protected FeatureSettings featureSettings = null;
private float heightScale = 1, widthScale = 1;
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
calculator = new jalview.workers.AlignCalcManager2();
this.applet = applet;
// we always pad gaps
this.setPadGaps(true);
if (applet != null)
{
// get the width and height scaling factors if they were specified
String param = applet.getParameter("widthScale");
if (param != null)
{
try
{
widthScale = Float.valueOf(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 = Float.valueOf(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, true);
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);
showOccupancy = applet.getDefaultParameter("showOccupancy",
showOccupancy);
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 = al.isNucleotide()
? applet.getParameter("defaultColourNuc")
: applet.getParameter("defaultColourProt");
if (colour == null)
{
colour = applet.getParameter("defaultColour");
}
if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
if (colour != null)
{
colour = "User Defined";
}
}
if (colour != null)
{
residueShading = new ResidueShader(ColourSchemeProperty
.getColourScheme(this, alignment, colour));
if (residueShading != null)
{
residueShading.setConsensus(consensusProfiles);
}
}
if (applet.getParameter("userDefinedColour") != null)
{
residueShading = new ResidueShader(new UserColourScheme(
applet.getParameter("userDefinedColour")));
}
}
initAutoAnnotation();
}
/**
* {@inheritDoc}
*/
@Override
public void setFont(Font f, boolean setGrid)
{
font = f;
if (nullFrame == null)
{
nullFrame = new java.awt.Frame();
nullFrame.addNotify();
}
if (setGrid)
{
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());
FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
setCharWidth(
(int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
public Font getFont()
{
return font;
}
public void resetSeqLimits(int height)
{
ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
}
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;
}
@Override
public void sendSelection()
{
getStructureSelectionManager().sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()), this);
}
/**
* Returns an instance of the StructureSelectionManager scoped to this applet
* instance.
*
* @return
*/
@Override
public StructureSelectionManager getStructureSelectionManager()
{
return jalview.structure.StructureSelectionManager
.getStructureSelectionManager(applet);
}
/**
*
* @return true if alignment characters should be displayed
*/
@Override
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);
notifyAlignment();
// 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.
*/
SearchResultsI sr = new SearchResults();
int seqOffset = findComplementScrollTarget(sr);
if (!sr.isEmpty())
{
complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, seqOffset);
complementPanel.setToScrollComplementPanel(true);
}
}
/**
* Applies the supplied feature settings descriptor to currently known
* features. This supports an 'initial configuration' of feature colouring
* based on a preset or user favourite. This may then be modified in the usual
* way using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
@Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
// TODO implement for applet
}
/**
* Merges the supplied feature settings descriptor with existing feature
* styles. This supports an 'initial configuration' of feature colouring based
* on a preset or user favourite. This may then be modified in the usual way
* using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
@Override
public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
{
// TODO Auto-generated method stub
}
}