From af3f78bc4a4f10b6a43d4fe109e07d0da462a571 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 6 May 2005 10:20:26 +0000
Subject: [PATCH] tidy
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2450 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/FeatureDisplay.java | 113 ++++++------------
1 file changed, 39 insertions(+), 74 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index a1a66d360..5d8919322 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.23 2005-05-05 14:50:39 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.24 2005-05-06 10:20:26 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.JComponent;
* This component is used for displaying an Entry.
*
* @author Kim Rutherford
- * @version $Id: FeatureDisplay.java,v 1.23 2005-05-05 14:50:39 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.24 2005-05-06 10:20:26 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -351,16 +351,6 @@ public class FeatureDisplay extends EntryGroupPanel
setBackground(Color.white);
}
- /**
- * Returns the value of a flag that indicates whether this component can be
- * traversed using Tab or Shift-Tab keyboard focus traversal - returns true
- * for FeatureDisplay components
- **/
-// tjc - deprecated replaced by isFocusable().
-//public boolean isFocusTraversable()
-//{
-// return true;
-//}
/**
* Overriden to call fixCanvasSize()
@@ -1107,8 +1097,8 @@ public class FeatureDisplay extends EntryGroupPanel
* true
**/
private void makeBaseVisibleInternal(final int base_position,
- final boolean forward,
- final boolean send_event)
+ final boolean forward,
+ final boolean send_event)
{
int forward_base_position = base_position;
@@ -1129,8 +1119,8 @@ public class FeatureDisplay extends EntryGroupPanel
private void makeBaseVisible(final Marker base_marker)
{
makeBaseVisibleInternal(base_marker.getPosition(),
- base_marker.getStrand().isForwardStrand(),
- true);
+ base_marker.getStrand().isForwardStrand(),
+ true);
}
/**
@@ -1150,7 +1140,7 @@ public class FeatureDisplay extends EntryGroupPanel
private void add(Feature feature)
{
if(getEntryGroup().isActive(feature.getEntry()) &&
- featureVisible(feature))
+ featureVisible(feature))
{
if(visible_features.contains(feature))
{
@@ -1368,7 +1358,7 @@ public class FeatureDisplay extends EntryGroupPanel
// filter out low and high scoring features and (possibly) source
// features
- for(int i = features_from_entry.size() - 1 ; i >= 0 ; --i)
+ for(int i = features_from_entry.size() - 1; i >= 0; --i)
{
final Feature this_feature = features_from_entry.elementAt(i);
@@ -1558,7 +1548,7 @@ public class FeatureDisplay extends EntryGroupPanel
private void fillLane(Graphics g, int fill_line_number,
int first_visible_base_coord, int last_visible_base_coord)
{
- int fill_line_top = fill_line_number*getLineHeight() + 1;
+ int fill_line_top = fill_line_number*getFontHeight() + 1;
g.fillRect(first_visible_base_coord, fill_line_top,
last_visible_base_coord - first_visible_base_coord + 1,
@@ -1575,7 +1565,7 @@ public class FeatureDisplay extends EntryGroupPanel
g.setColor(Color.black);
final int scale_line = getFrameDisplayLine(SCALE_LINE);
- final int scale_number_y_pos = scale_line * getLineHeight();
+ final int scale_number_y_pos = scale_line * getFontHeight();
final float bases_per_pixel =
(float)getMaxVisibleBases()/getWidth();
@@ -1624,10 +1614,9 @@ public class FeatureDisplay extends EntryGroupPanel
index_of_last_label =
getLastVisibleForwardBase() / base_label_spacing;
-// g.setFont(getFont());
final int font_ascent = getFontAscent();
final int font_width = getFontWidth();
- final int font_line_hgt = getLineHeight();
+ final int font_line_hgt = getFontHeight();
for(int i = index_of_first_label; i <= index_of_last_label; ++i)
{
@@ -1644,20 +1633,20 @@ public class FeatureDisplay extends EntryGroupPanel
getLowXPositionOfBase(i * base_label_spacing);
g.drawString(label_string,
- scale_number_x_pos + 2,
- scale_number_y_pos + font_ascent + 1);
+ scale_number_x_pos + 2,
+ scale_number_y_pos + font_ascent + 1);
g.drawLine(scale_number_x_pos, scale_number_y_pos,
- scale_number_x_pos, scale_number_y_pos + font_line_hgt);
+ scale_number_x_pos, scale_number_y_pos + font_line_hgt);
if(isRevCompDisplay())
g.drawLine(scale_number_x_pos, scale_number_y_pos,
- scale_number_x_pos + font_width, scale_number_y_pos);
+ scale_number_x_pos + font_width, scale_number_y_pos);
else
g.drawLine(scale_number_x_pos,
- scale_number_y_pos + font_line_hgt,
- scale_number_x_pos + font_width,
- scale_number_y_pos + font_line_hgt);
+ scale_number_y_pos + font_line_hgt,
+ scale_number_x_pos + font_width,
+ scale_number_y_pos + font_line_hgt);
}
}
@@ -1702,7 +1691,7 @@ public class FeatureDisplay extends EntryGroupPanel
offset = 0;
g.setFont(getFont());
- int yposition = forward_frame_line * getLineHeight();
+ int yposition = forward_frame_line * getFontHeight();
// draw fwd bases
if(getScaleFactor() == 0)
@@ -1726,7 +1715,7 @@ public class FeatureDisplay extends EntryGroupPanel
final int reverse_frame_line = getFrameDisplayLine(REVERSE_STRAND);
final int reverse_sequence_length = reverse_visible_bases.length();
- yposition = reverse_frame_line * getLineHeight();
+ yposition = reverse_frame_line * getFontHeight();
// draw bwd bases
if(getScaleFactor() == 0)
@@ -1787,7 +1776,6 @@ public class FeatureDisplay extends EntryGroupPanel
drawCodons(g,true);
if(show_reverse_lines)
- // drawReverseCodons(g);
drawCodons(g,false);
}
}
@@ -1827,9 +1815,6 @@ public class FeatureDisplay extends EntryGroupPanel
else
strand = getBases().getReverseStrand();
first_visible_base = getFirstVisibleReverseBase();
- // base to end translation at
- // we + 3 to the upper bound because partial codons do not get translated
- // by getTranslation()
end_base = getLastVisibleReverseBase() + 3;
}
@@ -2006,7 +1991,7 @@ public class FeatureDisplay extends EntryGroupPanel
offset = 0;
codons = codons.toUpperCase();
- final int draw_y_position = line_number * getLineHeight();
+ final int draw_y_position = line_number * getFontHeight();
final int draw_x_position;
if(direction == REVERSE)
@@ -2024,7 +2009,7 @@ public class FeatureDisplay extends EntryGroupPanel
}
/**
- * Draw one line of codons marks(stop codons or start codons).
+ * Draw one line of codons marks (stop codons or start codons).
* @param g The object to draw into.
* @param line_number The frame line to draw into. (see
* getFrameDisplayLine() for more details about these line numbers).
@@ -2047,7 +2032,7 @@ public class FeatureDisplay extends EntryGroupPanel
final int last_visible_forward_base = getLastVisibleForwardBase();
final double scale_value = getScaleValue();
- final int line_height = getLineHeight();
+ final int line_height = getFontHeight();
final Integer colour_number =
Options.getOptions().getIntegerProperty("colour_of_start_codon");
@@ -2188,7 +2173,7 @@ public class FeatureDisplay extends EntryGroupPanel
int x_pos, int y_pos)
{
g.setColor(getColourOfBase(base_char));
- g.drawLine(x_pos, y_pos, x_pos, y_pos + getLineHeight() - 1);
+ g.drawLine(x_pos, y_pos, x_pos, y_pos + getFontHeight() - 1);
}
/**
@@ -2271,7 +2256,7 @@ public class FeatureDisplay extends EntryGroupPanel
/**
* Return the line on the canvas where the given feature should be drawn
* when one_line_per_entry is true. Call getLineCount() to find out the
- * total number of lines. Each line is getLineHeight() pixels high.
+ * total number of lines. Each line is getFontHeight() pixels high.
* @return The line to draw into.
**/
private int getFeatureDisplayLine(final Feature feature,
@@ -2364,7 +2349,7 @@ public class FeatureDisplay extends EntryGroupPanel
/**
* Return the line on the canvas where this frame ID should be drawn. Call
* getLineCount() to find out the total number of lines. Each line is
- * getLineHeight() pixels high.
+ * getFontHeight() pixels high.
* @param frame_id The frame ID.
* @return The line to draw into.
**/
@@ -2577,7 +2562,7 @@ public class FeatureDisplay extends EntryGroupPanel
**/
private int getLineOffset(int line)
{
- return line * getLineHeight();
+ return line * getFontHeight();
}
/**
@@ -2899,10 +2884,6 @@ public class FeatureDisplay extends EntryGroupPanel
{
// if the feature border flag is off and the feature is not selected
// then don't draw the border
-// if(!show_feature_borders && !draw_feature_fill)
-// return;
-
-
highlight_feature_flag = false;
}
@@ -3121,7 +3102,7 @@ public class FeatureDisplay extends EntryGroupPanel
getSegmentVerticalOffset(first_segment);
if(show_labels)
- vertical_offset += getLineHeight(); // move to the label line
+ vertical_offset += getFontHeight(); // move to the label line
// save this so we can restore it later
Shape saved_clip = null;
@@ -3137,7 +3118,7 @@ public class FeatureDisplay extends EntryGroupPanel
g.fillRect(label_x_coord - getFontWidth(),
vertical_offset+2,
string_width + getFontWidth() * 2,
- getLineHeight()-1);
+ getFontHeight()-1);
}
else
{
@@ -3558,7 +3539,6 @@ public class FeatureDisplay extends EntryGroupPanel
**/
private void addListeners()
{
-
addMouseListener(new MouseAdapter()
{
private FeaturePopup popup = null;
@@ -3855,7 +3835,7 @@ public class FeatureDisplay extends EntryGroupPanel
}
if(Options.getOptions().canDirectEdit() &&
- !clicked_feature.isReadOnly())
+ !clicked_feature.isReadOnly())
{
// check to see if the click was on a marker, the second argument is
// false because we want the range to cover just one base
@@ -3907,10 +3887,10 @@ public class FeatureDisplay extends EntryGroupPanel
private Feature getFeatureOf(final Object object)
{
if(object instanceof Feature)
- return(Feature) object;
+ return (Feature)object;
else
// object must be a FeatureSegment
- return((FeatureSegment) object).getFeature();
+ return ((FeatureSegment)object).getFeature();
}
/**
@@ -4239,7 +4219,7 @@ public class FeatureDisplay extends EntryGroupPanel
private void fixCanvasSize()
{
int new_width = getSize().width;
- int new_height = getLineHeight() * getLineCount();
+ int new_height = getFontHeight() * getLineCount();
if(scale_changer != null)
new_width += scale_changer.getPreferredSize().height;
@@ -4289,15 +4269,6 @@ public class FeatureDisplay extends EntryGroupPanel
}
}
- /**
- * Return the height each line of the display should be. Each frame will
- * be drawn into one line.
- **/
- private int getLineHeight()
- {
- return getFontHeight();
- }
-
/**
* Return the current scale factor. The scale factor is a number greater
* than or equal to zero than controls the number of bases that can appear
@@ -4331,12 +4302,6 @@ public class FeatureDisplay extends EntryGroupPanel
}
- private int getDisplayHeight()
- {
- return getHeight() - scrollbar.getHeight();
- }
-
-
protected int getDisplayWidth()
{
return getWidth() - scale_changer.getWidth();
@@ -4349,10 +4314,10 @@ public class FeatureDisplay extends EntryGroupPanel
**/
private int getLineFromPoint(final Point point)
{
- if(point.y >= getDisplayHeight())
+ if(point.y >= getHeight() - scrollbar.getHeight())
return -1;
- final int return_value = point.y / getLineHeight();
+ final int return_value = point.y / getFontHeight();
if(return_value < 0)
return -1;
@@ -4392,9 +4357,9 @@ public class FeatureDisplay extends EntryGroupPanel
final int line_height;
if(show_labels)
- line_height = getLineHeight() * 2;
+ line_height = getFontHeight() * 2;
else
- line_height = getLineHeight();
+ line_height = getFontHeight();
if(point.y >= top_of_line &&
point.y < top_of_line + line_height)
@@ -4536,7 +4501,7 @@ public class FeatureDisplay extends EntryGroupPanel
**/
private int getFeatureHeight()
{
- // don't use getLineHeight() because we want a nice space between
+ // we want a nice space between
// frames/lines
return getFontAscent() + 2;
}
@@ -4547,7 +4512,7 @@ public class FeatureDisplay extends EntryGroupPanel
**/
protected int getMaxVisibleBases()
{
- return(int)(getWidth() / getScaleValue());
+ return (int)(getWidth()/getScaleValue());
}
/**
--
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