label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
+label.togglehidden = Toggle hidden columns on/off
\ No newline at end of file
warn.name_cannot_be_duplicate = Los nombres URL definidos por el usuario deben ser únicos y no pueden ser ids de MIRIAM
label.invalid_name = Nombre inválido !
label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
-label.urllinks = Enlaces
\ No newline at end of file
+label.urllinks = Enlaces
+label.togglehidden = Toggle hidden columns on/off
\ No newline at end of file
*/
package jalview.appletgui;
-import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsWithHidden;
import java.awt.BorderLayout;
import java.awt.Dimension;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
{
- private OverviewDimensions od;
+ private OverviewDimensionsWithHidden od;
private OverviewCanvas oviewCanvas;
this.ap = alPanel;
setLayout(null);
- od = new OverviewDimensions(av.getRanges(),
+ od = new OverviewDimensionsWithHidden(av.getRanges(),
(av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
oviewCanvas = new OverviewCanvas(od, av);
--- /dev/null
+/*
+ * 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.datamodel;
+
+import java.util.Iterator;
+
+public class AlignmentColsCollection implements Iterable<Integer>
+{
+ int start;
+ int end;
+ ColumnSelection hidden;
+
+ public AlignmentColsCollection(int s, int e, ColumnSelection colsel)
+ {
+ start = s;
+ end = e;
+ hidden = colsel;
+ }
+
+ @Override
+ public Iterator<Integer> iterator()
+ {
+ return new AllColsIterator(start,end,hidden);
+ }
+
+ /**
+ * Answers if the column at the the current position is hidden.
+ */
+ public boolean isHidden(int c)
+ {
+ return !hidden.isVisible(c);
+ }
+}
--- /dev/null
+/*
+ * 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.datamodel;
+
+import java.util.Iterator;
+
+public class AlignmentRowsCollection implements Iterable<Integer>
+{
+ int start;
+
+ int end;
+
+ AlignmentI alignment;
+
+ HiddenSequences hidden;
+
+ public AlignmentRowsCollection(int s, int e, AlignmentI al)
+ {
+ start = s;
+ end = e;
+ alignment = al;
+ hidden = al.getHiddenSequences();
+ }
+
+ @Override
+ public Iterator<Integer> iterator()
+ {
+ return new AllRowsIterator(start, end, alignment);
+ }
+
+ /**
+ * Answers if the sequence at the position is hidden.
+ */
+ public boolean isHidden(int seq)
+ {
+ return hidden.isHidden(seq);
+ }
+
+ public SequenceI getSequence(int seq)
+ {
+ return alignment.getSequenceAtAbsoluteIndex(seq);
+ }
+}
+
return false;
}
+
+ /**
+ * Answers if a sequence is hidden
+ *
+ * @param seq
+ * (absolute) index to test
+ * @return true if sequence at index seq is hidden
+ */
+ public boolean isHidden(int seq)
+ {
+ if (hiddenSequences != null)
+ {
+ return (hiddenSequences[seq] != null);
+ }
+ return false;
+ }
}
package jalview.gui;
import jalview.api.AlignViewportI;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.viewmodel.OverviewDimensions;
private jalview.renderer.seqfeatures.FeatureRenderer fr;
- private final AnnotationRenderer renderer = new AnnotationRenderer();
-
OverviewDimensions od;
AlignViewportI av;
fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
}
+ public void resetOviewDims(OverviewDimensions overviewDims)
+ {
+ od = overviewDims;
+ }
+
/*
* Signals to drawing code that the associated alignment viewport
* has changed and a redraw will be required
{
fr.transferSettings(transferRenderer);
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
// why do we need to set preferred size again? was set in
// updateOverviewImage
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
- miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ OverviewRenderer or = new OverviewRenderer(sr, finder, od);
+ miniMe = or.draw(od.getRows(av.getRanges(), av.getAlignment()),
+ od.getColumns(av.getRanges(), av.getColumnSelection()));
Graphics mg = miniMe.getGraphics();
- mg.setColor(Color.orange);
- mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
-
- // calculate sampleCol and sampleRow
- // alignment width is max number of residues/bases
- // alignment height is number of sequences
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getAbsoluteHeight();
-
- // sampleCol or sampleRow is the width/height allocated to each residue
- // in particular, sometimes we may need more than one row/col of the
- // BufferedImage allocated
- // sampleCol is how much of a residue to assign to each pixel
- // sampleRow is how many sequences to assign to each pixel
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-
- buildImage(sampleRow, sampleCol);
if (showAnnotation)
{
- renderer.updateFromAlignViewport(av);
- for (int col = 0; col < od.getWidth() && !restart; col++)
- {
- mg.translate(col, od.getSequencesHeight());
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, od.getGraphHeight(),
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -od.getSequencesHeight());
-
- }
+ mg.translate(0, od.getSequencesHeight());
+ or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getCharWidth(), od.getGraphHeight(),
+ od.getColumns(av.getRanges(), av.getColumnSelection()));
+ mg.translate(0, -od.getSequencesHeight());
}
System.gc();
od.drawBox(g);
}
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol)
- {
- int lastcol = -1;
- int lastrow = -1;
- int rgbcolor = Color.white.getRGB();
-
- SequenceI seq = null;
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
- // get hidden row and hidden column map once at beginning.
- // clone featureRenderer settings to avoid race conditions... if state is
- // updated just need to refresh again
- for (int row = 0; row < od.getSequencesHeight() && !restart; row++)
- {
- boolean doCopy = true;
- int currentrow = (int) (row * sampleRow);
- if (currentrow != lastrow)
- {
- doCopy = false;
-
- lastrow = currentrow;
-
- // get the sequence which would be at alignment index 'lastrow' if no
- // rows were hidden, and determine whether it is hidden or not
- hiddenRow = av.getAlignment().isHidden(lastrow);
- seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
- }
-
- for (int col = 0; col < od.getWidth() && !restart; col++)
- {
- if (doCopy)
- {
- rgbcolor = miniMe.getRGB(col, row - 1);
- }
- else if ((int) (col * sampleCol) != lastcol
- || (int) (row * sampleRow) != lastrow)
- {
- lastcol = (int) (col * sampleCol);
- rgbcolor = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol, finder);
- }
- // else we just use the color we already have , so don't need to set it
-
- miniMe.setRGB(col, row, rgbcolor);
- }
- }
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol,
- FeatureColourFinder finder)
- {
- Color color = Color.white;
-
- if ((seq != null) && (seq.getLength() > lastcol))
- {
- color = sr.getResidueColour(seq, lastcol, finder);
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
-
- return color.getRGB();
- }
-
}
*/
package jalview.gui;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsAllVisible;
+import jalview.viewmodel.OverviewDimensionsWithHidden;
import java.awt.BorderLayout;
import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
+import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
/**
* Panel displaying an overview of the full alignment, with an interactive box
private AlignmentPanel ap;
+ private boolean showHidden = true;
+
/**
* Creates a new OverviewPanel object.
*
this.av = alPanel.av;
this.ap = alPanel;
- od = new OverviewDimensions(av.getRanges(),
+ od = new OverviewDimensionsWithHidden(av.getRanges(),
(av.isShowAnnotation() && av
.getAlignmentConservationAnnotation() != null));
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (!SwingUtilities.isRightMouseButton(evt)
+ && !av.getWrapAlignment())
{
od.updateViewportFromMouse(evt.getX(), evt.getY(), av
.getAlignment().getHiddenSequences(), av
@Override
public void mousePressed(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ if (!Platform.isAMac())
+ {
+ showPopupMenu(evt);
+ }
+ }
+ else if (!av.getWrapAlignment())
{
od.updateViewportFromMouse(evt.getX(), evt.getY(), av
.getAlignment().getHiddenSequences(), av
ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
}
}
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ showPopupMenu(evt);
+ }
+ }
});
+
+ updateOverviewImage();
+ }
+
+ /*
+ * Displays the popup menu and acts on user input
+ */
+ private void showPopupMenu(MouseEvent e)
+ {
+ JPopupMenu popup = new JPopupMenu();
+ ActionListener menuListener = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent event)
+ {
+ // switch on/off the hidden columns view
+ toggleHiddenColumns();
+ }
+ };
+ JMenuItem item;
+ popup.add(item = new JMenuItem(MessageManager
+ .getString("label.togglehidden")));
+ item.addActionListener(menuListener);
+ popup.show(this, e.getX(), e.getY());
+ }
+
+ private void toggleHiddenColumns()
+ {
+ if (showHidden)
+ {
+ showHidden = false;
+ od = new OverviewDimensionsAllVisible(av.getRanges(),
+ (av.isShowAnnotation() && av
+ .getAlignmentConservationAnnotation() != null));
+ }
+ else
+ {
+ showHidden = true;
+ od = new OverviewDimensionsWithHidden(av.getRanges(),
+ (av.isShowAnnotation() && av
+ .getAlignmentConservationAnnotation() != null));
+ }
+ oviewCanvas.resetOviewDims(od);
updateOverviewImage();
}
--- /dev/null
+/*
+ * 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.gui;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentColsCollection;
+import jalview.datamodel.AlignmentRowsCollection;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.viewmodel.OverviewDimensions;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+
+public class OverviewRenderer
+{
+ private FeatureColourFinder finder;
+
+ private SequenceRenderer sr;
+
+ // image to render on
+ private BufferedImage miniMe;
+
+ // raw number of pixels to allocate to each column
+ private float pixelsPerCol;
+
+ // raw number of pixels to allocate to each row
+ private float pixelsPerSeq;
+
+ public OverviewRenderer(SequenceRenderer seqRenderer,
+ FeatureColourFinder colfinder, OverviewDimensions od)
+ {
+ sr = seqRenderer;
+ finder = colfinder;
+
+ pixelsPerCol = od.getPixelsPerCol();
+ pixelsPerSeq = od.getPixelsPerSeq();
+ miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ }
+
+ /**
+ * Draw alignment rows and columns onto an image
+ *
+ * @param rit
+ * Iterator over rows to be drawn
+ * @param cit
+ * Iterator over columns to be drawn
+ * @return image containing the drawing
+ */
+ public BufferedImage draw(AlignmentRowsCollection rows,
+ AlignmentColsCollection cols)
+ {
+ int rgbcolor = Color.white.getRGB();
+ int seqIndex = 0;
+ int pixelRow = 0;
+ for (int alignmentRow : rows)
+ {
+ // get details of this alignment row
+ boolean hidden = rows.isHidden(alignmentRow);
+ SequenceI seq = rows.getSequence(alignmentRow);
+
+ // calculate where this row extends to in pixels
+ int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
+ miniMe.getHeight() - 1);
+
+ int colIndex = 0;
+ int pixelCol = 0;
+ for (int alignmentCol : cols)
+ {
+ // calculate where this column extends to in pixels
+ int endCol = Math.min(
+ Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ miniMe.getWidth() - 1);
+
+ // determine the colour based on the sequence and column position
+ rgbcolor = getColumnColourFromSequence(seq,
+ hidden || cols.isHidden(alignmentCol), alignmentCol, finder);
+
+ // fill in the appropriate number of pixels
+ for (int row = pixelRow; row <= endRow; ++row)
+ {
+ for (int col = pixelCol; col <= endCol; ++col)
+ {
+ miniMe.setRGB(col, row, rgbcolor);
+ }
+ }
+
+ pixelCol = endCol + 1;
+ colIndex++;
+ }
+ pixelRow = endRow + 1;
+ seqIndex++;
+ }
+ return miniMe;
+ }
+
+ /*
+ * Find the colour of a sequence at a specified column position
+ */
+ private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
+ boolean isHidden, int lastcol, FeatureColourFinder finder)
+ {
+ Color color = Color.white;
+
+ if ((seq != null) && (seq.getLength() > lastcol))
+ {
+ color = sr.getResidueColour(seq, lastcol, finder);
+ }
+
+ if (isHidden)
+ {
+ color = color.darker().darker();
+ }
+
+ return color.getRGB();
+ }
+
+ public void drawGraph(Graphics g, AlignmentAnnotation _aa, int charWidth,
+ int y, AlignmentColsCollection cols)
+ {
+ Annotation[] aa_annotations = _aa.annotations;
+ g.setColor(Color.white);
+ g.fillRect(0, 0, miniMe.getWidth(), y);
+ // g.setColor(new Color(0, 0, 180));
+
+ int height;
+
+ int colIndex = 0;
+ int pixelCol = 0;
+ for (int alignmentCol : cols)
+ {
+ int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ miniMe.getWidth() - 1);
+
+ if (alignmentCol < aa_annotations.length
+ && aa_annotations[alignmentCol] != null)
+ {
+ if (aa_annotations[alignmentCol].colour == null)
+ {
+ g.setColor(Color.black);
+ }
+ else
+ {
+ g.setColor(aa_annotations[alignmentCol].colour);
+ }
+
+ height = (int) ((aa_annotations[alignmentCol].value / _aa.graphMax) * y);
+ if (height > y)
+ {
+ height = y;
+ }
+
+ g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
+ }
+ pixelCol = endCol + 1;
+ colIndex++;
+ }
+ }
+}
-/*
- * 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.viewmodel;
+import jalview.datamodel.AlignmentColsCollection;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentRowsCollection;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
import java.awt.Graphics;
-public class OverviewDimensions
+public abstract class OverviewDimensions
{
- // Default width and height values
- private static final int DEFAULT_GRAPH_HEIGHT = 20;
-
- private static final int MAX_WIDTH = 400;
-
- private static final int MIN_WIDTH = 120;
-
- private static final int MIN_SEQ_HEIGHT = 40;
-
- private static final int MAX_SEQ_HEIGHT = 300;
-
- // width of the overview panel
- private int width;
-
- // height of sequences part of the overview panel
- private int sequencesHeight;
-
- // height of the graphs part of the overview panel
- private int graphHeight = DEFAULT_GRAPH_HEIGHT;
-
- // dimensions of box outlining current extent of view in alignment panel
- // location of left side of box
- private int boxX = -1;
-
- // location of bottom of box
- private int boxY = -1;
- // width of box
- private int boxWidth = -1;
-
- // height of box
- private int boxHeight = -1;
-
- // scroll position in viewport corresponding to boxX
- private int scrollCol = -1;
-
- // scroll position in viewport corresponding to boxY
- private int scrollRow = -1;
+ private static final int DEFAULT_GRAPH_HEIGHT = 20;
+ protected static final int MAX_WIDTH = 400;
+ protected static final int MIN_WIDTH = 120;
+ protected static final int MIN_SEQ_HEIGHT = 40;
+ protected static final int MAX_SEQ_HEIGHT = 300;
+ protected int width;
+ protected int sequencesHeight;
+ protected int graphHeight = DEFAULT_GRAPH_HEIGHT;
+ protected int boxX = -1;
+ protected int boxY = -1;
+ protected int boxWidth = -1;
+ protected int boxHeight = -1;
+ protected int scrollCol = -1;
+ protected int scrollRow = -1;
- /**
- * Create an OverviewDimensions object
- *
- * @param ranges
- * positional properties of the viewport
- * @param showAnnotationPanel
- * true if the annotation panel is to be shown, false otherwise
- */
public OverviewDimensions(ViewportRanges ranges,
boolean showAnnotationPanel)
{
}
/**
- * Check box dimensions and scroll positions and correct if necessary
- *
- * @param mousex
- * x position in overview panel
- * @param mousey
- * y position in overview panel
- * @param hiddenSeqs
- * hidden sequences
- * @param hiddenCols
- * hidden columns
- * @param ranges
- * viewport position properties
- */
- public void updateViewportFromMouse(int mousex, int mousey,
- HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
- ViewportRanges ranges)
- {
- int x = mousex;
- int y = mousey;
-
- int alwidth = ranges.getAbsoluteAlignmentWidth();
- int alheight = ranges.getAbsoluteAlignmentHeight();
-
- if (x < 0)
- {
- x = 0;
- }
-
- if (y < 0)
- {
- y = 0;
- }
-
- //
- // Convert x value to residue position
- //
-
- // need to determine where scrollCol should be, given x
- // to do this also need to know width of viewport, and some hidden column
- // correction
-
- // convert x to residues - this is an absolute position
- int xAsRes = Math.round((float) x * alwidth / width);
-
- // get viewport width in residues
- int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
-
- // get where x should be when accounting for hidden cols
- // if x is in a hidden col region, shift to left - but we still need
- // absolute position
- // so convert back after getting visible region position
- int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
-
- // check in case we went off the edge of the alignment
- int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
- if (visXAsRes + vpwidth - 1 > visAlignWidth)
- {
- // went past the end of the alignment, adjust backwards
-
- // if last position was before the end of the alignment, need to update
- if ((scrollCol + vpwidth - 1) < visAlignWidth)
- {
- visXAsRes = hiddenCols.findColumnPosition(hiddenCols
- .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
- }
- else
- {
- visXAsRes = scrollCol;
- }
- }
-
- //
- // Convert y value to sequence position
- //
-
- // convert y to residues
- int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
-
- // get viewport height in sequences
- // add 1 because height includes both endSeq and startSeq
- int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
-
- // get where y should be when accounting for hidden rows
- // if y is in a hidden row region, shift up - but we still need absolute
- // position,
- // so convert back after getting visible region position
- yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
- .findIndexWithoutHiddenSeqs(yAsSeq));
-
- // check in case we went off the edge of the alignment
- int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
- int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
- if (visYAsRes + vpheight - 1 > visAlignHeight)
- {
- // went past the end of the alignment, adjust backwards
- if ((scrollRow + vpheight - 1) < visAlignHeight)
- {
- visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
- .subtractVisibleRows(vpheight - 1, alheight - 1));
- }
- else
- {
- visYAsRes = scrollRow;
- }
- }
-
- // update scroll values
- scrollCol = visXAsRes;
- scrollRow = visYAsRes;
-
- }
-
- /**
- * Update the overview panel box when the associated alignment panel is
- * changed
- *
- * @param hiddenSeqs
- * hidden sequences
- * @param hiddenCols
- * hidden columns
- * @param ranges
- * viewport position properties
- */
- public void setBoxPosition(HiddenSequences hiddenSeqs,
- ColumnSelection hiddenCols, ViewportRanges ranges)
- {
- int alwidth = ranges.getAbsoluteAlignmentWidth();
- int alheight = ranges.getAbsoluteAlignmentHeight();
-
- // work with absolute values of startRes and endRes
- int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
- int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
-
- // work with absolute values of startSeq and endSeq
- int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
- int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
-
- // boxX, boxY is the x,y location equivalent to startRes, startSeq
- boxX = Math.round((float) startRes * width / alwidth);
- boxY = Math.round((float) startSeq * sequencesHeight / alheight);
-
- // boxWidth is the width in residues translated to pixels
- // since the box includes both the start and end residues, add 1 to the
- // difference
- boxWidth = Math
- .round((float) (endRes - startRes + 1) * width / alwidth);
- // boxHeight is the height in sequences translated to pixels
- boxHeight = Math.round((float) (endSeq - startSeq + 1)
- * sequencesHeight
- / alheight);
- }
-
- /**
* Draw the overview panel's viewport box on a graphics object
*
* @param g
return scrollRow;
}
- // TODO should be removed, when unit test has mock Graphics object available
- // to check boxX/boxY
public int getBoxX()
{
return boxX;
}
- // TODO should be removed, when unit test has mock Graphics object available
- // to check boxX/boxY
public int getBoxY()
{
return boxY;
}
- // TODO should be removed, when unit test has mock Graphics object available
public int getBoxWidth()
{
return boxWidth;
}
- // TODO should be removed, when unit test has mock Graphics object available
public int getBoxHeight()
{
return boxHeight;
{
return graphHeight;
}
-}
+
+ public abstract void updateViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
+ ViewportRanges ranges);
+
+ public abstract void setBoxPosition(HiddenSequences hiddenSeqs,
+ ColumnSelection hiddenCols, ViewportRanges ranges);
+
+ public abstract AlignmentColsCollection getColumns(
+ ViewportRanges ranges, ColumnSelection hiddenCols);
+
+ public abstract AlignmentRowsCollection getRows(
+ ViewportRanges ranges, AlignmentI al);
+
+ public abstract float getPixelsPerCol();
+
+ public abstract float getPixelsPerSeq();
+}
\ No newline at end of file
--- /dev/null
+package jalview.viewmodel;
+
+import jalview.datamodel.AlignmentColsCollection;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentRowsCollection;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
+
+public class OverviewDimensionsAllVisible extends OverviewDimensions
+{
+ private float pixelsPerCol;
+
+ private float pixelsPerSeq;
+
+ public OverviewDimensionsAllVisible(ViewportRanges ranges,
+ boolean showAnnotationPanel)
+ {
+ super(ranges, showAnnotationPanel);
+
+ int alwidth = ranges.getVisibleAlignmentWidth();
+ int alheight = ranges.getVisibleAlignmentHeight();
+
+ pixelsPerCol = (float) width / alwidth;
+ pixelsPerSeq = (float) sequencesHeight / alheight;
+ }
+
+ @Override
+ public void updateViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
+ ViewportRanges ranges)
+ {
+ int x = mousex;
+ int y = mousey;
+
+ int alwidth = ranges.getVisibleAlignmentWidth();
+ int alheight = ranges.getVisibleAlignmentHeight();
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ //
+ // Convert x value to residue position
+ //
+
+ // need to determine where scrollCol should be, given x
+ // to do this also need to know width of viewport, and some hidden column
+ // correction
+
+ // convert x to residues - this is an absolute position
+ int xAsRes = Math.round((float) x * alwidth / width);
+
+ // get viewport width in residues
+ int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
+
+ if (xAsRes + vpwidth > alwidth)
+ {
+ // went past the end of the alignment, adjust backwards
+
+ // if last position was before the end of the alignment, need to update
+ if ((scrollCol + vpwidth - 1) < alwidth)
+ {
+ xAsRes = alwidth - vpwidth;
+ }
+ else
+ {
+ xAsRes = scrollCol;
+ }
+ }
+
+
+ //
+ // Convert y value to sequence position
+ //
+
+ // convert y to residues
+ int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+
+ // get viewport height in sequences
+ // add 1 because height includes both endSeq and startSeq
+ int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
+
+ if (yAsSeq + vpheight > alheight)
+ {
+ // went past the end of the alignment, adjust backwards
+ if ((scrollRow + vpheight - 1) < alheight)
+ {
+ yAsSeq = alheight - vpheight;
+ }
+ else
+ {
+ yAsSeq = scrollRow;
+ }
+ }
+
+ // update scroll values
+ scrollCol = xAsRes;
+ scrollRow = yAsSeq;
+
+ }
+
+ @Override
+ public void setBoxPosition(HiddenSequences hiddenSeqs,
+ ColumnSelection hiddenCols, ViewportRanges ranges)
+ {
+ int alwidth = ranges.getVisibleAlignmentWidth();
+ int alheight = ranges.getVisibleAlignmentHeight();
+
+ // work with visible values of startRes and endRes
+ int startRes = ranges.getStartRes();
+ int endRes = ranges.getEndRes();
+
+ // work with visible values of startSeq and endSeq
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
+
+ // boxX, boxY is the x,y location equivalent to startRes, startSeq
+ boxX = Math.round((float) startRes * width / alwidth);
+ boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+
+ // boxWidth is the width in residues translated to pixels
+ // since the box includes both the start and end residues, add 1 to the
+ // difference
+ boxWidth = Math
+ .round((float) (endRes - startRes + 1) * width / alwidth);
+ // boxHeight is the height in sequences translated to pixels
+ boxHeight = Math.round((float) (endSeq - startSeq + 1)
+ * sequencesHeight / alheight);
+
+ }
+
+ @Override
+ public AlignmentColsCollection getColumns(ViewportRanges ranges,
+ ColumnSelection hiddenCols)
+ {
+ return new AlignmentColsCollection(0,
+ ranges.getVisibleAlignmentWidth() - 1, hiddenCols);
+ }
+
+ @Override
+ public AlignmentRowsCollection getRows(ViewportRanges ranges,
+ AlignmentI al)
+ {
+ return new AlignmentRowsCollection(0,
+ ranges.getVisibleAlignmentHeight() - 1, al);
+ }
+
+ @Override
+ public float getPixelsPerCol()
+ {
+ return pixelsPerCol;
+ }
+
+ @Override
+ public float getPixelsPerSeq()
+ {
+ return pixelsPerSeq;
+ }
+}
--- /dev/null
+/*
+ * 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.viewmodel;
+
+import jalview.datamodel.AlignmentColsCollection;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentRowsCollection;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
+
+public class OverviewDimensionsWithHidden extends OverviewDimensions
+{
+ private float pixelsPerCol;
+
+ private float pixelsPerSeq;
+
+ /**
+ * Create an OverviewDimensions object
+ *
+ * @param ranges
+ * positional properties of the viewport
+ * @param showAnnotationPanel
+ * true if the annotation panel is to be shown, false otherwise
+ */
+ public OverviewDimensionsWithHidden(ViewportRanges ranges,
+ boolean showAnnotationPanel)
+ {
+ super(ranges, showAnnotationPanel);
+
+ int alwidth = ranges.getAbsoluteAlignmentWidth();
+ int alheight = ranges.getAbsoluteAlignmentHeight();
+
+ pixelsPerCol = (float) width / alwidth;
+ pixelsPerSeq = (float) sequencesHeight / alheight;
+ }
+
+ /**
+ * Check box dimensions and scroll positions and correct if necessary
+ *
+ * @param mousex
+ * x position in overview panel
+ * @param mousey
+ * y position in overview panel
+ * @param hiddenSeqs
+ * hidden sequences
+ * @param hiddenCols
+ * hidden columns
+ * @param ranges
+ * viewport position properties
+ */
+ @Override
+ public void updateViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
+ ViewportRanges ranges)
+ {
+ int x = mousex;
+ int y = mousey;
+
+ int alwidth = ranges.getAbsoluteAlignmentWidth();
+ int alheight = ranges.getAbsoluteAlignmentHeight();
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ //
+ // Convert x value to residue position
+ //
+
+ // need to determine where scrollCol should be, given x
+ // to do this also need to know width of viewport, and some hidden column
+ // correction
+
+ // convert x to residues - this is an absolute position
+ int xAsRes = Math.round((float) x * alwidth / width);
+
+ // get viewport width in residues
+ int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
+
+ // get where x should be when accounting for hidden cols
+ // if x is in a hidden col region, shift to left - but we still need
+ // absolute position
+ // so convert back after getting visible region position
+ int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+
+ // check in case we went off the edge of the alignment
+ int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+ if (visXAsRes + vpwidth - 1 > visAlignWidth)
+ {
+ // went past the end of the alignment, adjust backwards
+
+ // if last position was before the end of the alignment, need to update
+ if ((scrollCol + vpwidth - 1) < visAlignWidth)
+ {
+ visXAsRes = hiddenCols.findColumnPosition(hiddenCols
+ .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+ }
+ else
+ {
+ visXAsRes = scrollCol;
+ }
+ }
+
+ //
+ // Convert y value to sequence position
+ //
+
+ // convert y to residues
+ int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+
+ // get viewport height in sequences
+ // add 1 because height includes both endSeq and startSeq
+ int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
+
+ // get where y should be when accounting for hidden rows
+ // if y is in a hidden row region, shift up - but we still need absolute
+ // position,
+ // so convert back after getting visible region position
+ yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
+ .findIndexWithoutHiddenSeqs(yAsSeq));
+
+ // check in case we went off the edge of the alignment
+ int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+ int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+ if (visYAsSeq + vpheight - 1 > visAlignHeight)
+ {
+ // went past the end of the alignment, adjust backwards
+ if ((scrollRow + vpheight - 1) < visAlignHeight)
+ {
+ visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
+ .subtractVisibleRows(vpheight - 1, alheight - 1));
+ }
+ else
+ {
+ visYAsSeq = scrollRow;
+ }
+ }
+
+ // update scroll values
+ scrollCol = visXAsRes;
+ scrollRow = visYAsSeq;
+
+ }
+
+ /**
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
+ * @param hiddenSeqs
+ * hidden sequences
+ * @param hiddenCols
+ * hidden columns
+ * @param ranges
+ * viewport position properties
+ */
+ @Override
+ public void setBoxPosition(HiddenSequences hiddenSeqs,
+ ColumnSelection hiddenCols, ViewportRanges ranges)
+ {
+ int alwidth = ranges.getAbsoluteAlignmentWidth();
+ int alheight = ranges.getAbsoluteAlignmentHeight();
+
+ // work with absolute values of startRes and endRes
+ int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
+ int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+
+ // work with absolute values of startSeq and endSeq
+ int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
+ int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
+
+ // boxX, boxY is the x,y location equivalent to startRes, startSeq
+ boxX = Math.round((float) startRes * width / alwidth);
+ boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+
+ // boxWidth is the width in residues translated to pixels
+ // since the box includes both the start and end residues, add 1 to the
+ // difference
+ boxWidth = Math
+ .round((float) (endRes - startRes + 1) * width / alwidth);
+ // boxHeight is the height in sequences translated to pixels
+ boxHeight = Math.round((float) (endSeq - startSeq + 1)
+ * sequencesHeight
+ / alheight);
+ }
+
+ @Override
+ public AlignmentColsCollection getColumns(ViewportRanges ranges,
+ ColumnSelection hiddenCols)
+ {
+ return new AlignmentColsCollection(0,
+ ranges.getAbsoluteAlignmentWidth() - 1,
+ hiddenCols);
+ }
+
+ @Override
+ public AlignmentRowsCollection getRows(ViewportRanges ranges,
+ AlignmentI al)
+ {
+ return new AlignmentRowsCollection(0,
+ ranges.getAbsoluteAlignmentHeight() - 1,
+ al);
+ }
+
+ @Override
+ public float getPixelsPerCol()
+ {
+ return pixelsPerCol;
+ }
+
+ @Override
+ public float getPixelsPerSeq()
+ {
+ return pixelsPerSeq;
+ }
+}
}
/**
+ * Get alignment width in cols, excluding hidden cols
+ */
+ public int getVisibleAlignmentWidth()
+ {
+ // TODO need access to hidden columns here
+ return al.getWidth(); // - hidden columns
+ }
+
+ /**
+ * Get alignment height in rows, excluding hidden rows
+ */
+ public int getVisibleAlignmentHeight()
+ {
+ return al.getHeight();
+ }
+
+ /**
* Set first residue visible in the viewport
*
* @param res
public class OverviewDimensionsTest
{
AlignmentI al;
- OverviewDimensions od;
+ OverviewDimensionsWithHidden od;
// cached widths and heights
int boxWidth;
ColumnSelection hiddenCols = new ColumnSelection();
- od = new OverviewDimensions(vpranges, true);
+ od = new OverviewDimensionsWithHidden(vpranges, true);
// Initial box sizing - default path through code
od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
Alignment al1 = new Alignment(seqs1);
ViewportRanges props = new ViewportRanges(al1);
- OverviewDimensions od = new OverviewDimensions(props, true);
+ OverviewDimensions od = new OverviewDimensionsWithHidden(props, true);
int scaledHeight = 267;
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), scaledHeight);
Alignment al2 = new Alignment(seqs2);
props = new ViewportRanges(al2);
- od = new OverviewDimensions(props, true);
+ od = new OverviewDimensionsWithHidden(props, true);
int scaledWidth = 300;
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
Alignment al3 = new Alignment(seqs3);
props = new ViewportRanges(al3);
- od = new OverviewDimensions(props, true);
+ od = new OverviewDimensionsWithHidden(props, true);
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), minSeqHeight);
assertEquals(od.getWidth(), maxWidth);
Alignment al4 = new Alignment(seqs4);
props = new ViewportRanges(al4);
- od = new OverviewDimensions(props, true);
+ od = new OverviewDimensionsWithHidden(props, true);
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
assertEquals(od.getWidth(), minWidth);
Alignment al5 = new Alignment(seqs4);
props = new ViewportRanges(al5);
- od = new OverviewDimensions(props, false);
+ od = new OverviewDimensionsWithHidden(props, false);
assertEquals(od.getGraphHeight(), 0);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
assertEquals(od.getWidth(), minWidth);
/*
* Mouse click as position x,y in overview window
*/
- private void mouseClick(OverviewDimensions od, int x, int y)
+ private void mouseClick(OverviewDimensionsWithHidden od, int x, int y)
{
od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols,
vpranges);
git://source.jalview.org / jalview.git / commitdiff