/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
setGUINucleotide(viewport.getAlignment().isNucleotide());
}
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
int startPos = aligmentStartEnd[0];
int endPos = aligmentStartEnd[1];
- int[] lowestRange = new int[2];
- int[] higestRange = new int[2];
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
for (int[] hiddenCol : hiddenCols)
{
- // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
}
- // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
- // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
- if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
{
startPos = aligmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == 0 && higestRange[1] == 0)
+ if (higestRange[0] == -1 && higestRange[1] == -1)
{
endPos = aligmentStartEnd[1];
}
else
{
- endPos = higestRange[0];
+ endPos = higestRange[0] - 1;
}
- // System.out.println("Export range : " + minPos + " - " + maxPos);
+ // System.out.println("Export range : " + startPos + " - " + endPos);
return new int[] { startPos, endPos };
}
public static void main(String[] args)
{
ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
- hiddenCols.add(new int[] { 0, 4 });
+ hiddenCols.add(new int[] { 0, 0 });
hiddenCols.add(new int[] { 6, 9 });
hiddenCols.add(new int[] { 11, 12 });
hiddenCols.add(new int[] { 33, 33 });
- hiddenCols.add(new int[] { 45, 50 });
+ hiddenCols.add(new int[] { 50, 50 });
int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
// System.out.println("Export range : " + x[0] + " - " + x[1]);
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
{
- return;
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
-
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);