package jalview.viewmodel;
import jalview.api.AlignViewportI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
import java.awt.Graphics;
private AlignViewportI av;
- private float scalew = 1f;
-
- private float scaleh = 1f;
+ private ViewportPositionProps posProps;
// width of the overview panel
private int width;
private int scrollRow = -1;
- public OverviewDimensions(AlignViewportI avi)
+ public OverviewDimensions(AlignViewportI avi, boolean showAnnotationPanel)
{
this.av = avi;
+ this.posProps = av.getPosProps();
// scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.getAlignment().getWidth()
- / (float) av.getAlignment().getHeight();
+ float initialScale = (float) posProps.getAlignmentWidthInCols()
+ / (float) posProps.getAlignmentHeightInRows();
- // TODO: in applet this was getSequenceConsensusHash()
- // check if it makes any functional difference
- if (av.getAlignmentConservationAnnotation() == null)
+ if (!showAnnotationPanel)
{
graphHeight = 0;
}
- if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
+ if (posProps.getAlignmentWidthInCols() > posProps
+ .getAlignmentHeightInRows())
{
// wider
width = MAX_WIDTH;
/**
* Check box dimensions and scroll positions and correct if necessary
*/
- public void setBoxPositionByMouse(int x, int y)
+ public void updateViewportFromMouse(int x, int y)
{
- boxX = x;
- boxY = y;
- if (boxY < 0)
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getAbsoluteHeight();
+
+ HiddenSequences hiddenSeqs = av.getAlignment().getHiddenSequences();
+ ColumnSelection hiddenCols = av.getColumnSelection();
+
+ if (x < 0)
{
- boxY = 0;
+ x = 0;
}
- else if (boxY > (sequencesHeight - boxHeight))
+ else if (x >= alwidth)
{
- boxY = sequencesHeight - boxHeight + 1;
+ x = alwidth - 1;
}
- if (boxX < 0)
+ if (y < 0)
{
- boxX = 0;
+ y = 0;
}
- else if (boxX > (width - boxWidth))
+ else if (y >= alheight)
{
- if (av.hasHiddenColumns())
- {
- // Try smallest possible box
- boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1)
- * av.getCharWidth() * scalew);
- }
- boxX = width - boxWidth;
+ y = alheight - 1;
}
- scrollCol = (int) (boxX / scalew / av.getCharWidth());
- scrollRow = (int) (boxY / scaleh / av.getCharHeight());
+ //
+ // Convert x value to residue position
+ //
- if (av.hasHiddenColumns())
- {
- if (!av.getColumnSelection().isVisible(scrollCol))
- {
- return;
- }
+ // need to determine where scrollCol should be, given x
+ // to do this also need to know width of viewport, and some hidden column
+ // correction
- scrollCol = av.getColumnSelection().findColumnPosition(scrollCol);
- }
+ // convert x to residues - this is an absolute position
+ int xAsRes = Math.round((float) x * alwidth / width);
- if (av.hasHiddenRows())
- {
- scrollRow = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(scrollRow);
- }
- }
+ // get viewport width in residues
+ int vpwidth = av.getPosProps().getEndRes()
+ - av.getPosProps().getStartRes() + 1;
- /**
- * Update the overview panel box when the associated alignment panel is
- * changed
- *
- */
- public void setBoxPosition()
- {
- updateScales();
+ // 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
+ xAsRes = hiddenCols.adjustForHiddenColumns(hiddenCols
+ .findColumnPosition(xAsRes));
- int startRes = av.getStartRes();
- int endRes = av.getEndRes();
+ // get where end res should be by adding the viewport width on
+ int endRes = xAsRes + vpwidth;
- if (av.hasHiddenColumns())
+ // check in case we went off the edge of the alignment
+ if (endRes > alwidth)
{
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+ // went past the end of the alignment, adjust backwards
+ endRes = alwidth;
+ // recalc xAsRes backwards from endRes
+ xAsRes = endRes - vpwidth;
}
- int startSeq = av.getStartSeq();
- int endSeq = av.getEndSeq();
+ //
+ // Convert y value to sequence position
+ //
- if (av.hasHiddenRows())
- {
- startSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(startSeq);
+ // convert y to residues
+ int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
- endSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(endSeq);
- }
+ // get viewport height in sequences
+ int vpheight = av.getPosProps().getEndSeq()
+ - av.getPosProps().getStartSeq();
+
+ // 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));
- boxX = (int) (startRes * av.getCharWidth() * scalew);
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+ // get where end seq should be by adding the viewport height on
+ int endSeq = yAsSeq + vpheight;
+
+ // check in case we went off the edge of the alignment
+ if (endSeq > alheight)
+ {
+ // went past the end of the alignment, adjust backwards
+ endSeq = alheight;
+ // recalc yAsSeq backwards from endSeq
+ yAsSeq = endSeq - vpheight;
+ }
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
- boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+ // convert absolute positions back to visible alignment positions for
+ // viewport scrolling
+ scrollCol = hiddenCols.findColumnPosition(xAsRes);
+ scrollRow = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
}
/**
- * Update width and height scales in terms of the alignment width and height
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
*/
- public void updateScales()
+ public void setBoxPosition()
{
int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
+ int alheight = av.getAlignment().getAbsoluteHeight();
- int fullsizeWidth = alwidth * av.getCharWidth();
- int fullsizeHeight = alheight * av.getCharHeight();
+ int startRes = av.getPosProps().getAbsoluteStartRes();
+ int endRes = av.getPosProps().getAbsoluteEndRes();
- scalew = (float) width / fullsizeWidth;
- scaleh = (float) sequencesHeight / fullsizeHeight;
+ int startSeq = av.getPosProps().getAbsoluteStartSeq();
+ int endSeq = av.getPosProps().getAbsoluteEndSeq();
+
+ boxX = Math.round((float) startRes * width / alwidth);
+ boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+
+ boxWidth = Math
+ .round((float) (endRes - startRes + 1) * width / alwidth);
+ boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
+ / alheight);
}
/**
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;
git://source.jalview.org / jalview.git / blobdiff