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import java.awt.event.ItemListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
-import java.util.Hashtable;
public class FeatureColourChooser extends Panel implements ActionListener,
AdjustmentListener, ItemListener, MouseListener
{
- JVDialog frame;
+ /*
+ * the absolute min-max range of a feature score is scaled to
+ * 1000 positions on the colour threshold slider
+ */
+ private static final int SCALE_FACTOR_1K = 1000;
- Frame owner;
+ private JVDialog frame;
- FeatureRenderer fr;
+ private Frame owner;
- FeatureSettings fs = null;
+ private FeatureRenderer fr;
- // AlignmentPanel ap;
+ private FeatureSettings fs = null;
- FeatureColourI cs;
+ private FeatureColourI cs;
- FeatureColourI oldcs;
+ private FeatureColourI oldcs;
- Hashtable oldgroupColours;
-
- boolean adjusting = false;
+ private boolean adjusting = false;
private float min, max;
- String type = null;
+ private String type = null;
private AlignFrame af = null;
- public FeatureColourChooser(AlignFrame af, String type)
+ private Panel minColour = new Panel();
+
+ private Panel maxColour = new Panel();
+
+ private Choice threshold = new Choice();
+
+ private Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
+ private TextField thresholdValue = new TextField(20);
+
+ private Checkbox thresholdIsMin = new Checkbox();
+
+ private Checkbox colourFromLabel = new Checkbox();
+
+ private GraphLine threshline;
+
+ /**
+ * Constructor given a context AlignFrame and a feature type. This is used
+ * when opening the graduated colour dialog from the Amend Feature dialog.
+ *
+ * @param alignFrame
+ * @param featureType
+ */
+ public FeatureColourChooser(AlignFrame alignFrame, String featureType)
{
- this.af = af;
- init(af.getSeqcanvas().getFeatureRenderer(), type);
+ this.af = alignFrame;
+ init(alignFrame.getSeqcanvas().getFeatureRenderer(), featureType);
}
- public FeatureColourChooser(FeatureSettings fsettings, String type)
+ /**
+ * Constructor given a context FeatureSettings and a feature type. This is
+ * used when opening the graduated colour dialog from Feature Settings.
+ *
+ * @param fsettings
+ * @param featureType
+ */
+ public FeatureColourChooser(FeatureSettings fsettings, String featureType)
{
this.fs = fsettings;
- init(fsettings.fr, type);
- // this.ap = fsettings.ap;
+ init(fsettings.fr, featureType);
}
- private void init(FeatureRenderer frenderer, String type)
+ private void init(FeatureRenderer frenderer, String featureType)
{
- this.type = type;
+ this.type = featureType;
fr = frenderer;
float mm[] = fr.getMinMax().get(type)[0];
min = mm[0];
: 0));
adjusting = false;
- changeColour();
+ changeColour(true);
colourFromLabel.addItemListener(this);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
frame.setVisible(true);
if (frame.accept)
{
- changeColour();
+ changeColour(true);
}
else
{
// cancel
reset();
- PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
frame.setVisible(false);
}
}
thresholdIsMin.addItemListener(this);
this.setLayout(new GridLayout(4, 1));
+ Panel jPanel1 = new Panel();
jPanel1.setLayout(new FlowLayout());
+ Panel jPanel2 = new Panel();
jPanel2.setLayout(new FlowLayout());
+ Panel jPanel3 = new Panel();
jPanel3.setLayout(new GridLayout(1, 1));
+ Panel jPanel4 = new Panel();
jPanel4.setLayout(new FlowLayout());
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
}
- Panel minColour = new Panel();
-
- Panel maxColour = new Panel();
-
- Panel jPanel1 = new Panel();
-
- Panel jPanel2 = new Panel();
-
- Choice threshold = new Choice();
-
- Panel jPanel3 = new Panel();
-
- Panel jPanel4 = new Panel();
-
- Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
-
- TextField thresholdValue = new TextField(20);
-
- // BorderLayout borderLayout1 = new BorderLayout();
-
- Checkbox thresholdIsMin = new Checkbox();
-
- Checkbox colourFromLabel = new Checkbox();
-
- private GraphLine threshline;
-
@Override
public void actionPerformed(ActionEvent evt)
{
try
{
float f = new Float(thresholdValue.getText()).floatValue();
- slider.setValue((int) (f * 1000));
+ slider.setValue((int) (f * SCALE_FACTOR_1K));
adjustmentValueChanged(null);
+
+ /*
+ * force repaint of any Overview window or structure
+ */
+ changeColour(true);
} catch (NumberFormatException ex)
{
}
}
else
{
- changeColour();
+ changeColour(true);
}
}
{
maxColour.setEnabled(!colourFromLabel.getState());
minColour.setEnabled(!colourFromLabel.getState());
- changeColour();
+ changeColour(true);
}
+ /**
+ * Handler called when the value of the threshold slider changes, either by
+ * user action or programmatically
+ */
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
}
}
+ /**
+ * Responds to a change of colour threshold by computing the absolute value
+ * and refreshing the alignment.
+ */
protected void valueChanged()
{
threshline.value = slider.getValue() / 1000f;
cs.setThreshold(threshline.value);
- changeColour();
+ changeColour(false);
PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
- // ap.paintAlignment(false);
}
public void minColour_actionPerformed(Color newCol)
{
if (newCol == null)
{
- UserDefinedColours udc = new UserDefinedColours(this,
+ new UserDefinedColours(this,
minColour.getBackground(), owner,
- MessageManager.getString("label.select_colour_minimum_value")); // frame.owner,
+ MessageManager.getString("label.select_colour_minimum_value"));
}
else
{
minColour.setBackground(newCol);
minColour.setForeground(newCol);
minColour.repaint();
- changeColour();
+ changeColour(true);
}
}
{
if (newCol == null)
{
-
- // UserDefinedColours udc = new UserDefinedColours(this,
- // "Select Colour for Maximum Value",maxColour.getBackground(),true);
- UserDefinedColours udc = new UserDefinedColours(this,
+ new UserDefinedColours(this,
maxColour.getBackground(), owner,
MessageManager.getString("label.select_colour_maximum_value"));
}
maxColour.setBackground(newCol);
maxColour.setForeground(newCol);
maxColour.repaint();
- changeColour();
+ changeColour(true);
}
}
- void changeColour()
+ void changeColour(boolean updateOverview)
{
// Check if combobox is still adjusting
if (adjusting)
return;
}
- int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+ int thresholdOption = AnnotationColourGradient.NO_THRESHOLD;
if (threshold.getSelectedIndex() == 1)
{
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ thresholdOption = AnnotationColourGradient.ABOVE_THRESHOLD;
}
else if (threshold.getSelectedIndex() == 2)
{
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ thresholdOption = AnnotationColourGradient.BELOW_THRESHOLD;
}
slider.setEnabled(true);
acg.setColourByLabel(colourFromLabel.getState());
maxColour.setEnabled(!colourFromLabel.getState());
minColour.setEnabled(!colourFromLabel.getState());
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ if (thresholdOption == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
}
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
{
adjusting = true;
acg.setThreshold(threshline.value);
- float range = max * 1000f - min * 1000f;
-
- slider.setMinimum((int) (min * 1000));
- slider.setMaximum((int) (max * 1000));
- slider.setValue((int) (threshline.value * 1000));
+ slider.setMinimum((int) (min * SCALE_FACTOR_1K));
+ slider.setMaximum((int) (max * SCALE_FACTOR_1K));
+ slider.setValue((int) (threshline.value * SCALE_FACTOR_1K));
thresholdValue.setText(threshline.value + "");
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
}
- acg.setAboveThreshold(true);
+ acg.setAboveThreshold(thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
+ acg.setBelowThreshold(thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
+
if (thresholdIsMin.getState()
- && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ && thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
{
- if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
{
acg = new FeatureColour(acg, threshline.value, max);
}
fr.setColour(type, acg);
cs = acg;
- PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
- // ap.paintAlignment(false);
+ fs.selectionChanged(updateOverview);
}
void reset()
{
fr.setColour(type, oldcs);
- PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
- // ap.paintAlignment(true);
-
+ fs.selectionChanged(true);
}
@Override
@Override
public void mouseReleased(MouseEvent evt)
{
- if (evt.getSource() == minColour || evt.getSource() == maxColour)
+ if (evt.getSource() == minColour)
{
- // relay the event
- actionPerformed(new ActionEvent(evt.getSource(), 1, "Clicked"));
+ minColour_actionPerformed(null);
+ }
+ else if (evt.getSource() == maxColour)
+ {
+ maxColour_actionPerformed(null);
}
else
{
- PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
+ changeColour(true);
+ // PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
}
- // ap.paintAlignment(true);
}
@Override
Checkbox check = (Checkbox) featurePanel.getComponent(i);
check.setState(!check.getState());
}
- selectionChanged();
+ selectionChanged(true);
}
private ItemListener groupItemListener = new ItemListener()
@Override
public void itemStateChanged(ItemEvent evt)
{
- selectionChanged();
+ selectionChanged(true);
}
- void selectionChanged()
+ void selectionChanged(boolean updateOverview)
{
Component[] comps = featurePanel.getComponents();
int cSize = comps.length;
fr.setFeaturePriority(data);
- ap.paintAlignment(true);
+ ap.paintAlignment(updateOverview);
}
MyCheckbox selectedCheck;
import java.awt.BorderLayout;
import java.awt.CheckboxMenuItem;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Panel;
import java.awt.PopupMenu;
private boolean updateRunning = false;
+ private boolean draggingBox = false;
+
public OverviewPanel(AlignmentPanel alPanel)
{
this.av = alPanel.av;
@Override
public void mouseMoved(MouseEvent evt)
{
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ }
}
@Override
public void mousePressed(MouseEvent evt)
{
- mouseAction(evt);
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ if (!Platform.isAMac())
+ {
+ showPopupMenu(evt);
+ }
+ }
+ else
+ {
+ if (!od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // don't do anything if the mouse press is in the overview's box
+ // (wait to see if it's a drag instead)
+ // otherwise update the viewport
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ draggingBox = true;
+ od.setDragPoint(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ }
}
@Override
public void mouseReleased(MouseEvent evt)
{
- mouseAction(evt);
+ if (draggingBox)
+ {
+ draggingBox = false;
+ }
}
@Override
public void mouseDragged(MouseEvent evt)
{
- mouseAction(evt);
- }
-
- private void mouseAction(MouseEvent evt)
- {
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
if (!Platform.isAMac())
}
else
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
- .getHiddenSequences(), av.getAlignment().getHiddenColumns());
+ if (draggingBox)
+ {
+ // set the mouse position as a fixed point in the box
+ // and drag relative to that position
+ od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
ap.paintAlignment(false);
}
}
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
*/
public class PaintRefresher
{
- static Hashtable components;
+ static Map<String, Vector<Component>> components;
/**
* DOCUMENT ME!
{
if (components == null)
{
- components = new Hashtable();
+ components = new Hashtable<String, Vector<Component>>();
}
if (components.containsKey(seqSetId))
{
- Vector comps = (Vector) components.get(seqSetId);
+ Vector<Component> comps = components.get(seqSetId);
if (!comps.contains(comp))
{
comps.addElement(comp);
}
else
{
- Vector vcoms = new Vector();
+ Vector<Component> vcoms = new Vector<>();
vcoms.addElement(comp);
components.put(seqSetId, vcoms);
}
return;
}
- Enumeration en = components.keys();
- while (en.hasMoreElements())
+ for (String id : components.keySet())
{
- String id = en.nextElement().toString();
- Vector comps = (Vector) components.get(id);
+ Vector<Component> comps = components.get(id);
comps.removeElement(comp);
if (comps.size() == 0)
{
}
Component comp;
- Vector comps = (Vector) components.get(id);
+ Vector<Component> comps = components.get(id);
if (comps == null)
{
return;
}
- Enumeration e = comps.elements();
+ Enumeration<Component> e = comps.elements();
while (e.hasMoreElements())
{
- comp = (Component) e.nextElement();
+ comp = e.nextElement();
if (comp == source)
{
public static AlignmentPanel[] getAssociatedPanels(String id)
{
- Vector comps = (Vector) components.get(id);
- Vector tmp = new Vector();
+ Vector<Component> comps = components.get(id);
+ Vector<Component> tmp = new Vector<>();
int i, iSize = comps.size();
for (i = 0; i < iSize; i++)
{
return startRow - visibleDistance;
}
- int index = startRow;
+ int index = Math.min(startRow, hiddenSequences.length - 1);
int count = 0;
while ((index > -1) && (count < visibleDistance))
{
public class FeatureColourChooser extends JalviewDialog
{
// FeatureSettings fs;
- FeatureRenderer fr;
+ private FeatureRenderer fr;
private FeatureColourI cs;
private FeatureColourI oldcs;
- /**
- *
- * @return the last colour setting selected by user - either oldcs (which may
- * be a java.awt.Color) or the new GraduatedColor
- */
- public FeatureColourI getLastColour()
- {
- if (cs == null)
- {
- return oldcs;
- }
- return cs;
- }
+ private AlignmentPanel ap;
- AlignmentPanel ap;
-
- boolean adjusting = false;
+ private boolean adjusting = false;
final private float min;
final private float scaleFactor;
- String type = null;
+ private String type = null;
+
+ private JPanel minColour = new JPanel();
+
+ private JPanel maxColour = new JPanel();
- public FeatureColourChooser(FeatureRenderer frender, String type)
+ private JComboBox<String> threshold = new JComboBox<>();
+
+ private JSlider slider = new JSlider();
+
+ private JTextField thresholdValue = new JTextField(20);
+
+ // TODO implement GUI for tolower flag
+ // JCheckBox toLower = new JCheckBox();
+
+ private JCheckBox thresholdIsMin = new JCheckBox();
+
+ private JCheckBox colourByLabel = new JCheckBox();
+
+ private GraphLine threshline;
+
+ private Color oldmaxColour;
+
+ private Color oldminColour;
+
+ private ActionListener colourEditor = null;
+
+ /**
+ * Constructor
+ *
+ * @param frender
+ * @param theType
+ */
+ public FeatureColourChooser(FeatureRenderer frender, String theType)
{
- this(frender, false, type);
+ this(frender, false, theType);
}
- public FeatureColourChooser(FeatureRenderer frender, boolean block,
- String type)
+ /**
+ * Constructor, with option to make a blocking dialog (has to complete in the
+ * AWT event queue thread). Currently this option is always set to false.
+ *
+ * @param frender
+ * @param blocking
+ * @param theType
+ */
+ FeatureColourChooser(FeatureRenderer frender, boolean blocking,
+ String theType)
{
this.fr = frender;
- this.type = type;
+ this.type = theType;
ap = fr.ap;
String title = MessageManager.formatMessage(
- "label.graduated_color_for_params", new String[] { type });
- initDialogFrame(this, true, block, title, 480, 185);
- // frame.setLayer(JLayeredPane.PALETTE_LAYER);
- // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
- // 480, 145);
+ "label.graduated_color_for_params", new String[] { theType });
+ initDialogFrame(this, true, blocking, title, 480, 185);
slider.addChangeListener(new ChangeListener()
{
if (!adjusting)
{
thresholdValue.setText((slider.getValue() / scaleFactor) + "");
- valueChanged();
+ sliderValueChanged();
}
}
});
@Override
public void mouseReleased(MouseEvent evt)
{
+ /*
+ * only update Overview and/or structure colouring
+ * when threshold slider drag ends (mouse up)
+ */
if (ap != null)
{
ap.paintAlignment(true);
}
- ;
}
});
- float mm[] = fr.getMinMax().get(type)[0];
+ float mm[] = fr.getMinMax().get(theType)[0];
min = mm[0];
max = mm[1];
*/
scaleFactor = (max == min) ? 1f : 100f / (max - min);
- oldcs = fr.getFeatureColours().get(type);
+ oldcs = fr.getFeatureColours().get(theType);
if (!oldcs.isSimpleColour())
{
if (oldcs.isAutoScaled())
adjusting = false;
- changeColour();
+ changeColour(false);
waitForInput();
}
}
});
maxColour.setBorder(new LineBorder(Color.black));
- minText.setText(MessageManager.getString("label.min"));
+ JLabel minText = new JLabel(MessageManager.getString("label.min"));
minText.setFont(JvSwingUtils.getLabelFont());
- maxText.setText(MessageManager.getString("label.max"));
+ JLabel maxText = new JLabel(MessageManager.getString("label.max"));
maxText.setFont(JvSwingUtils.getLabelFont());
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
jPanel1.setBackground(Color.white);
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setLayout(new FlowLayout());
jPanel2.setBackground(Color.white);
threshold.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- threshold_actionPerformed(e);
+ threshold_actionPerformed();
}
});
threshold.setToolTipText(MessageManager
.getString("label.threshold_feature_above_threshold")); // index 1
threshold.addItem(MessageManager
.getString("label.threshold_feature_below_threshold")); // index 2
- jPanel3.setLayout(flowLayout2);
+
+ JPanel jPanel3 = new JPanel();
+ jPanel3.setLayout(new FlowLayout());
thresholdValue.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- thresholdValue_actionPerformed(e);
+ thresholdValue_actionPerformed();
}
});
slider.setPaintLabels(false);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- thresholdIsMin_actionPerformed(actionEvent);
+ thresholdIsMin_actionPerformed();
}
});
colourByLabel.setBackground(Color.white);
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- colourByLabel_actionPerformed(actionEvent);
+ colourByLabel_actionPerformed();
}
});
+
+ JPanel colourPanel = new JPanel();
colourPanel.setBackground(Color.white);
jPanel1.add(ok);
jPanel1.add(cancel);
- jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
- jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
+ jPanel2.add(colourByLabel, BorderLayout.WEST);
+ jPanel2.add(colourPanel, BorderLayout.EAST);
colourPanel.add(minText);
colourPanel.add(minColour);
colourPanel.add(maxText);
colourPanel.add(maxColour);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ this.add(jPanel3, BorderLayout.CENTER);
jPanel3.add(threshold);
jPanel3.add(slider);
jPanel3.add(thresholdValue);
jPanel3.add(thresholdIsMin);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ this.add(jPanel1, BorderLayout.SOUTH);
+ this.add(jPanel2, BorderLayout.NORTH);
}
- JLabel minText = new JLabel();
-
- JLabel maxText = new JLabel();
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JPanel colourPanel = new JPanel();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- JComboBox threshold = new JComboBox();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- JPanel jPanel3 = new JPanel();
-
- FlowLayout flowLayout2 = new FlowLayout();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- // TODO implement GUI for tolower flag
- // JCheckBox toLower = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox colourByLabel = new JCheckBox();
-
- private GraphLine threshline;
-
- private Color oldmaxColour;
-
- private Color oldminColour;
-
- public void minColour_actionPerformed()
+ /**
+ * Action on clicking the 'minimum colour' - open a colour chooser dialog, and
+ * set the selected colour (if the user does not cancel out of the dialog)
+ */
+ protected void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_minimum_value"),
minColour.setForeground(col);
}
minColour.repaint();
- changeColour();
+ changeColour(true);
}
- public void maxColour_actionPerformed()
+ /**
+ * Action on clicking the 'maximum colour' - open a colour chooser dialog, and
+ * set the selected colour (if the user does not cancel out of the dialog)
+ */
+ protected void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_maximum_value"),
maxColour.setForeground(col);
}
maxColour.repaint();
- changeColour();
+ changeColour(true);
}
- void changeColour()
+ /**
+ * Constructs and sets the selected colour options as the colour for the
+ * feature type, and repaints the alignment, and optionally the Overview
+ * and/or structure viewer if open
+ *
+ * @param updateOverview
+ */
+ void changeColour(boolean updateOverview)
{
// Check if combobox is still adjusting
if (adjusting)
{
acg = new FeatureColour(oldminColour = minColour.getBackground(),
oldmaxColour = maxColour.getBackground(), min, max);
-
}
if (!hasThreshold)
}
else if (threshline == null)
{
- // todo visual indication of feature threshold
+ /*
+ * todo not yet implemented: visual indication of feature threshold
+ */
threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
}
slider.setMinimum((int) (min * scaleFactor));
slider.setMaximum((int) (max * scaleFactor));
- slider.setValue((int) (threshline.value * scaleFactor));
+ // slider.setValue((int) (threshline.value * scaleFactor));
+ slider.setValue(Math.round(threshline.value * scaleFactor));
thresholdValue.setText(threshline.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
}
fr.setColour(type, acg);
cs = acg;
- ap.paintAlignment(false);
+ ap.paintAlignment(updateOverview);
}
@Override
@Override
public void okPressed()
{
- changeColour();
+ changeColour(false);
}
@Override
reset();
}
+ /**
+ * Action when the user cancels the dialog. All previous settings should be
+ * restored and rendered on the alignment, and any linked Overview window or
+ * structure.
+ */
void reset()
{
fr.setColour(type, oldcs);
- ap.paintAlignment(false);
+ ap.paintAlignment(true);
cs = null;
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
+ /**
+ * Action on change of choice of No / Above / Below Threshold
+ */
+ protected void threshold_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ /**
+ * Action on text entry of a threshold value
+ */
+ protected void thresholdValue_actionPerformed()
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
slider.setValue((int) (f * scaleFactor));
threshline.value = f;
+
+ /*
+ * force repaint of any Overview window or structure
+ */
+ ap.paintAlignment(true);
} catch (NumberFormatException ex)
{
}
}
- public void valueChanged()
+ /**
+ * Action on change of threshold slider value. This may be done interactively
+ * (by moving the slider), or programmatically (to update the slider after
+ * manual input of a threshold value).
+ */
+ protected void sliderValueChanged()
{
- threshline.value = slider.getValue() / scaleFactor;
+ /*
+ * squash rounding errors by forcing min/max of slider to
+ * actual min/max of feature score range
+ */
+ int value = slider.getValue();
+ threshline.value = value == slider.getMaximum() ? max
+ : (value == slider.getMinimum() ? min : value / scaleFactor);
cs.setThreshold(threshline.value);
- changeColour();
- ap.paintAlignment(false);
+
+ /*
+ * repaint alignment, but not Overview or structure,
+ * to avoid overload while dragging the slider
+ */
+ changeColour(false);
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ protected void thresholdIsMin_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- public void colourByLabel_actionPerformed(ActionEvent actionEvent)
+ protected void colourByLabel_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- ActionListener colourEditor = null;
-
- public void addActionListener(ActionListener graduatedColorEditor)
+ void addActionListener(ActionListener graduatedColorEditor)
{
if (colourEditor != null)
{
colourEditor = graduatedColorEditor;
}
+ /**
+ * Answers the last colour setting selected by user - either oldcs (which may
+ * be a java.awt.Color) or the new GraduatedColor
+ *
+ * @return
+ */
+ FeatureColourI getLastColour()
+ {
+ if (cs == null)
+ {
+ return oldcs;
+ }
+ return cs;
+ }
+
}
{
av.getRanges().scrollRight(true);
}
- else
+ else if (!av.getWrapAlignment())
{
av.getRanges().scrollUp(false);
}
{
av.getRanges().scrollRight(false);
}
- else
+ else if (!av.getWrapAlignment())
{
av.getRanges().scrollUp(true);
}
import jalview.viewmodel.ViewportListenerI;
import java.awt.BorderLayout;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
private boolean showHidden = true;
+ private boolean draggingBox = false;
+
/**
* Creates a new OverviewPanel object.
*
{
if (!SwingUtilities.isRightMouseButton(evt))
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+ if (draggingBox)
+ {
+ // set the mouse position as a fixed point in the box
+ // and drag relative to that position
+ od.adjustViewportFromMouse(evt.getX(),
+ evt.getY(), av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ od.updateViewportFromMouse(evt.getX(), evt.getY(), av
.getAlignment().getHiddenSequences(), av.getAlignment()
.getHiddenColumns());
+ }
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
}
}
});
else
// if (!av.getWrapAlignment())
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av.getAlignment()
- .getHiddenColumns());
+ if (!od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // don't do anything if the mouse press is in the overview's box
+ // (wait to see if it's a drag instead)
+ // otherwise update the viewport
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ draggingBox = true;
+ od.setDragPoint(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (draggingBox)
+ {
+ draggingBox = false;
}
}
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
/**
+ * Update the viewport location from a mouse drag within the overview's box
+ *
+ * @param mousex
+ * x location of mouse
+ * @param mousey
+ * y location of mouse
+ * @param hiddenSeqs
+ * the alignment's hidden sequences
+ * @param hiddenCols
+ * the alignment's hidden columns
+ */
+ public abstract void adjustViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
+
+ /**
+ * Initialise dragging from the mouse - must be called on initial mouse click
+ * before using adjustViewportFromMouse in drag operations
+ *
+ * @param mousex
+ * x location of mouse
+ * @param mousey
+ * y location of mouse
+ * @param hiddenSeqs
+ * the alignment's hidden sequences
+ * @param hiddenCols
+ * the alignment's hidden columns
+ */
+ public abstract void setDragPoint(int x, int y,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
+
+ /*
+ * Move the viewport so that the top left corner of the overview's box
+ * is at the mouse position (leftx, topy)
+ */
+ protected abstract void updateViewportFromTopLeft(int leftx, int topy,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
+
+ /**
* Set the overview panel's box position to match the viewport
*
* @param hiddenSeqs
*/
protected abstract void resetAlignmentDims();
+ /*
+ * Given the box coordinates in residues and sequences, set the box dimensions in the overview window
+ */
protected void setBoxPosition(int startRes, int startSeq, int vpwidth,
int vpheight)
{
// boxHeight is the height in sequences translated to pixels
boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
}
+
+ /**
+ * Answers if a mouse position is in the overview's red box
+ *
+ * @param x
+ * mouse x position
+ * @param y
+ * mouse y position
+ * @return true if (x,y) is inside the box
+ */
+ public boolean isPositionInBox(int x, int y)
+ {
+ return (x > boxX && y > boxY && x < boxX + boxWidth
+ && y < boxY + boxHeight);
+ }
+
+ /*
+ * Given the centre x position, calculate the box's left x position
+ */
+ protected abstract int getLeftXFromCentreX(int mousex, HiddenColumns hidden);
+
+ /*
+ * Given the centre y position, calculate the box's top y position
+ */
+ protected abstract int getTopYFromCentreY(int mousey,
+ HiddenSequences hidden);
+
}
\ No newline at end of file
{
private ViewportRanges ranges;
+ private int xdiff; // when dragging, difference in alignment units between
+ // start residue and original mouse click position
+
+ private int ydiff; // when dragging, difference in alignment units between
+ // start sequence and original mouse click position
+
public OverviewDimensionsHideHidden(ViewportRanges vpranges,
boolean showAnnotationPanel)
{
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
- resetAlignmentDims();
+ int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
+ int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
+
+ updateViewportFromTopLeft(xAsRes, yAsSeq, hiddenSeqs, hiddenCols);
+
+ }
+
+ @Override
+ public void adjustViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
+ {
+ // calculate translation in pixel terms:
+ // get mouse location in viewport coords, add translation in viewport
+ // coords, and update viewport as usual
+ int vpx = Math.round((float) mousex * alwidth / width);
+ int vpy = Math.round((float) mousey * alheight / sequencesHeight);
- int x = mousex;
- int y = mousey;
+ updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs,
+ hiddenCols);
- if (x < 0)
+ }
+
+ @Override
+ protected void updateViewportFromTopLeft(int leftx, int topy,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
+ {
+ int xAsRes = leftx;
+ int yAsSeq = topy;
+ resetAlignmentDims();
+
+ if (xAsRes < 0)
{
- x = 0;
+ xAsRes = 0;
}
- if (y < 0)
+ if (yAsSeq < 0)
{
- y = 0;
+ yAsSeq = 0;
}
if (ranges.isWrappedMode())
{
- y = 0; // sorry, no vertical scroll when wrapped
+ yAsSeq = 0; // sorry, no vertical scroll when wrapped
}
- //
- // 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.getViewportWidth();
}
}
-
- //
- // Convert y value to sequence position
- //
-
- // convert y to residues
- int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+ // Determine where scrollRow should be, given visYAsSeq
// get viewport height in sequences
// add 1 because height includes both endSeq and startSeq
// update viewport
ranges.setStartRes(xAsRes);
ranges.setStartSeq(yAsSeq);
-
}
@Override
alwidth = ranges.getVisibleAlignmentWidth();
alheight = ranges.getVisibleAlignmentHeight();
}
+
+ @Override
+ protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
+ {
+ int vpx = Math.round((float) mousex * alwidth / width);
+ return vpx - ranges.getViewportWidth() / 2;
+ }
+
+ @Override
+ protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
+ {
+ int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ return vpy - ranges.getViewportHeight() / 2;
+ }
+
+ @Override
+ public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
+ HiddenColumns hiddenCols)
+ {
+ // get alignment position of x and box (can get directly from vpranges) and
+ // calculate difference between the positions
+ int vpx = Math.round((float) x * alwidth / width);
+ int vpy = Math.round((float) y * alheight / sequencesHeight);
+
+ xdiff = ranges.getStartRes() - vpx;
+ ydiff = ranges.getStartSeq() - vpy;
+ }
+
}
{
private ViewportRanges ranges;
+ private int xdiff; // when dragging, difference in alignment units between
+ // start residue and original mouse click position
+
+ private int ydiff; // when dragging, difference in alignment units between
+ // start sequence and original mouse click position
+
/**
* Create an OverviewDimensions object
*
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
- int x = mousex;
- int y = mousey;
+ // convert mousex and mousey to alignment units as well as
+ // translating to top left corner of viewport - this is an absolute position
+ int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
+ int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
- resetAlignmentDims();
+ // convert to visible positions
+ int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+ yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
+ hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
+ yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
+ int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+ visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
- if (x < 0)
- {
- x = 0;
- }
+ // update viewport accordingly
+ updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
+ }
+
+ @Override
+ public void adjustViewportFromMouse(int mousex, int mousey,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
+ {
+ // calculate translation in pixel terms:
+ // get mouse location in viewport coords, add translation in viewport
+ // coords,
+ // convert back to pixel coords
+ int vpx = Math.round((float) mousex * alwidth / width);
+ int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
+
+ int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
+
+ // update viewport accordingly
+ updateViewportFromTopLeft(visXAsRes, visYAsRes,
+ hiddenSeqs,
+ hiddenCols);
+ }
+
+ @Override
+ protected void updateViewportFromTopLeft(int leftx, int topy,
+ HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
+ {
+ int visXAsRes = leftx;
+ int visYAsSeq = topy;
+ resetAlignmentDims();
- if (y < 0)
+ if (visXAsRes < 0)
{
- y = 0;
+ visXAsRes = 0;
}
- if (ranges.isWrappedMode())
+ if (visYAsSeq < 0)
{
- y = 0; // sorry, no vertical scroll when wrapped
+ visYAsSeq = 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);
+ // Determine where scrollCol should be, given visXAsRes
// get viewport width in residues
int vpwidth = ranges.getViewportWidth();
- // 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)
}
}
- //
- // Convert y value to sequence position
- //
-
- // convert y to residues
- int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+ // Determine where scrollRow should be, given visYAsSeq
// get viewport height in sequences
int vpheight = ranges.getViewportHeight();
- // 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));
- yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
-
// check in case we went off the edge of the alignment
int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
- int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
- visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
+
if (visYAsSeq + vpheight - 1 > visAlignHeight)
{
// went past the end of the alignment, adjust backwards
alwidth = ranges.getAbsoluteAlignmentWidth();
alheight = ranges.getAbsoluteAlignmentHeight();
}
+
+ @Override
+ protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
+ {
+ int vpx = Math.round((float) mousex * alwidth / width);
+ return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+ vpx);
+ }
+
+ @Override
+ protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
+ {
+ int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
+ }
+
+ @Override
+ public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
+ HiddenColumns hiddenCols)
+ {
+ // get alignment position of x and box (can get directly from vpranges) and
+ // calculate difference between the positions
+ int vpx = Math.round((float) x * alwidth / width);
+ int vpy = Math.round((float) y * alheight / sequencesHeight);
+
+ xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
+ ydiff = ranges.getStartSeq()
+ - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
+ }
+
}
* updated - JAL-1904), and verify (some) feature group colours
*/
colours = af.getFeatureRenderer().getFeatureColours();
- assertEquals("26 feature group colours not found", 26, colours.size());
+ assertEquals("27 feature group colours not found", 27, colours.size());
assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+ FeatureColourI kdColour = colours.get("kdHydrophobicity");
+ assertTrue(kdColour.isGraduatedColour());
+ assertTrue(kdColour.isAboveThreshold());
+ assertEquals(-2f, kdColour.getThreshold());
/*
* verify (some) features on sequences
package jalview.viewmodel;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
import jalview.analysis.AlignmentGenerator;
import jalview.datamodel.Alignment;
ViewportRanges vpranges;
- Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
HiddenColumns hiddenCols = new HiddenColumns();
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartSeq(),
+ assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
Math.round((float) 10 * alheight / od.getSequencesHeight()));
assertEquals(vpranges.getStartRes(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) 6 * alwidth / od.getWidth()));
+ assertEquals(vpranges.getStartRes(), 0);
assertEquals(vpranges.getStartSeq(), 0);
// overly large boxX value reset to width-boxWidth
- mouseClick(od, 100, 6);
+ mouseClick(od, 101, 6);
assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
- assertEquals(od.getBoxY(), 6);
+ assertEquals(od.getBoxY(), 1);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
// overly large boxY value reset to sequenceHeight - boxHeight
mouseClick(od, 10, 520);
- assertEquals(od.getBoxX(), 10);
+ assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
/ od.getSequencesHeight()));
// move viewport so startRes non-zero and then mouseclick
- moveViewportH(50);
+ moveViewportH(20);
// click at viewport position
int oldboxx = od.getBoxX();
int oldboxy = od.getBoxY();
- mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
- assertEquals(od.getBoxX(), oldboxx + 5);
+ mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
+ od.getBoxY() + od.getBoxHeight() / 2 + 3);
+ assertEquals(od.getBoxX(), oldboxx + 6);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(od.getBoxY(), oldboxy + 2);
+ assertEquals(od.getBoxY(), oldboxy + 3);
assertEquals(
vpranges.getStartSeq(),
Math.round((float) od.getBoxY() * alheight
int lastHiddenCol = 30;
hiddenCols.hideColumns(0, lastHiddenCol);
- testBoxIsAtClickPoint(0, 0);
+ testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
// click to right of hidden columns, box moves to click point
- testBoxIsAtClickPoint(40, 0);
+ testBoxIsAtClickPoint(41 + boxWidth / 2, boxHeight / 2);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(),
- Math.round((float) 40 * alwidth / od.getWidth()));
+ Math.round((float) 41 * alwidth / od.getWidth()));
// click to right of hidden columns such that box runs over right hand side
// of alignment
// box position is adjusted away from the edge
// overly large boxX value reset to width-boxWidth
- int xpos = 100;
- mouseClick(od, xpos, 0);
+ int xpos = 100 + boxWidth / 2;
+ mouseClick(od, xpos, boxHeight / 2);
assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
public void testFromMouseWithHiddenColsInMiddle()
{
od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
- testBoxIsAtClickPoint(0, 0);
+ testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
hiddenCols.hideColumns(firstHidden, lastHidden);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
- testBoxIsAtClickPoint(0, 0);
+ testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// move box so that it overlaps with hidden cols on one side
// box width, boxX and scrollCol as for unhidden case
- int xpos = 55 - boxWidth; // 55 is position in overview approx halfway
+ int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
// between cols 60 and 70
- mouseClick(od, xpos, 0);
- testBoxIsAtClickPoint(xpos, 0);
- assertEquals(vpranges.getStartRes(),
- Math.round(xpos * alwidth / od.getWidth()));
+ mouseClick(od, xpos, boxHeight / 2);
+ testBoxIsAtClickPoint(xpos, boxHeight / 2);
+ assertEquals(vpranges.getStartRes(), 1 + // rounding
+ Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// move box so that it completely covers hidden cols
// box width, boxX and scrollCol as for unhidden case
xpos = 33;
- mouseClick(od, xpos, 0);
- testBoxIsAtClickPoint(xpos, 0);
+ mouseClick(od, xpos, boxHeight / 2);
+ testBoxIsAtClickPoint(xpos, boxHeight / 2);
assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
+ Math.round((float) (xpos - boxWidth / 2) * alwidth
+ / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// move box so boxX is in hidden cols, box overhangs at right
// boxX and scrollCol at left of hidden area, box width unchanged
- xpos = 50;
- mouseClick(od, xpos, 0);
- testBoxIsAtClickPoint(xpos, 0);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
+ xpos = Math.round((float) 50 * od.getWidth() / alwidth) + boxWidth / 2;
+ mouseClick(od, xpos, boxHeight / 2);
+ assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(vpranges.getStartRes(), 50);
assertEquals(vpranges.getStartSeq(), 0);
// move box so boxX is to right of hidden cols, but does not go beyond full
// width of alignment
// box width, boxX and scrollCol all as for non-hidden case
- xpos = 75;
- testBoxIsAtClickPoint(xpos, 0);
+ xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
+ mouseClick(od, xpos, boxHeight / 2);
+ assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
- assertEquals(vpranges.getStartRes(),
- Math.round(xpos * alwidth / od.getWidth()));
+ assertEquals(vpranges.getStartRes(), 75);
// move box so it goes beyond full width of alignment
// boxX, scrollCol adjusted back, box width normal
xpos = 3000;
- mouseClick(od, xpos, 0);
+ mouseClick(od, xpos, boxHeight / 2);
assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// click to left of hidden cols, without overlapping
// boxX, scrollCol and width as normal
- int xpos = 5;
- testBoxIsAtClickPoint(xpos, 0);
- assertEquals(vpranges.getStartSeq(), 0);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
+ int xpos = 30;
+ int ypos = 6;
+ testBoxIsAtClickPoint(xpos, ypos);
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
+ assertEquals(vpranges.getStartRes(), Math.round(
+ (float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
// click to left of hidden cols, with overlap
// boxX and scrollCol adjusted for hidden cols, width normal
- xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
- mouseClick(od, xpos, 0);
- testBoxIsAtClickPoint(xpos, 0);
+ xpos = Math.round((float) 144 * od.getWidth() / alwidth) - boxWidth;
+ mouseClick(od, xpos, boxHeight / 2);
+ testBoxIsAtClickPoint(xpos, boxHeight / 2);
assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
+ Math.round((float) (xpos - boxWidth / 2) * alwidth
+ / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// click off end of alignment
assertEquals(od.getBoxHeight(), boxHeight);
// click below hidden rows
- mouseClick(od, 0, 150);
+ mouseClick(od, 0, 151 + boxHeight / 2);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), 150);
+ assertEquals(od.getBoxY(), 151);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows, so that box overlaps
- int ypos = 35; // column value in residues
+ int ypos = 35 + viewHeight / 2; // row value in residues
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round((float) 35 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click so that box straddles hidden rows
- ypos = 44; // column value in residues
+ ypos = 45 + viewHeight / 2; // row value in residues
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round((float) 45 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows
- int ypos = 40; // row 40
+ int ypos = 41 + viewHeight / 2; // row 41
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round((float) 41 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows so box overlaps
// boxY, boxHeight remains same
- ypos = 497; // row 497
+ ypos = 497 + viewHeight / 2; // row 497
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxHeight(), boxHeight);
}
+ /**
+ * Test the function to determine if a point is in the overview's box or not
+ */
+ @Test(groups = { "Functional" })
+ public void testPositionInBox()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+
+ // hide columns in the box area
+ // makes absolutely no difference
+ hiddenCols.hideColumns(1, 4);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+
+ // hide sequences in box area
+ // makes absolutely no difference
+ hideSequences(1, 3);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+ }
+
+ /**
+ * Test the dragging functionality
+ */
+ @Test(groups = { "Functional" })
+ public void testDragging()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(),
+ hiddenCols);
+ od.adjustViewportFromMouse(20, 22,
+ al.getHiddenSequences(), hiddenCols);
+
+ // updates require an OverviewPanel to exist which it doesn't here
+ // so call setBoxPosition() as it would be called by the AlignmentPanel
+ // normally
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) right and 6 (22-16) up
+ assertEquals(od.getBoxX(), 16);
+ assertEquals(od.getBoxY(), 6);
+
+ // hide columns - makes no difference
+ hiddenCols.hideColumns(1, 4);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) right and 6 (22-16) up
+ assertEquals(od.getBoxX(), 16);
+ assertEquals(od.getBoxY(), 6);
+
+ // hide sequences in box area
+ // makes absolutely no difference
+ hideSequences(1, 3);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) right and 6 (22-16) up
+ assertEquals(od.getBoxX(), 16);
+ assertEquals(od.getBoxY(), 6);
+ }
+
/*
* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
*/
private void testBoxIsAtClickPoint(int xpos, int ypos)
{
mouseClick(od, xpos, ypos);
- assertEquals(od.getBoxX(), xpos);
- assertEquals(od.getBoxY(), ypos);
+ assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
+ assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
package jalview.viewmodel;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
import jalview.analysis.AlignmentGenerator;
import jalview.datamodel.Alignment;
ViewportRanges vpranges;
- Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
HiddenColumns hiddenCols = new HiddenColumns();
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartSeq(),
+ assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
Math.round((float) 10 * alheight / od.getSequencesHeight()));
assertEquals(vpranges.getStartRes(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) 6 * alwidth / od.getWidth()));
+ assertEquals(vpranges.getStartRes(), 0);
assertEquals(vpranges.getStartSeq(), 0);
// overly large boxX value reset to width-boxWidth
- mouseClick(od, 100, 6);
+ mouseClick(od, 101, 6);
assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
- assertEquals(od.getBoxY(), 6);
+ assertEquals(od.getBoxY(), 1);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
// overly large boxY value reset to sequenceHeight - boxHeight
mouseClick(od, 10, 520);
- assertEquals(od.getBoxX(), 10);
+ assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartRes(),
+ assertEquals(0,
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
/ od.getSequencesHeight()));
// move viewport so startRes non-zero and then mouseclick
- moveViewportH(50);
+ moveViewportH(20);
// click at viewport position
int oldboxx = od.getBoxX();
int oldboxy = od.getBoxY();
- mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
- assertEquals(od.getBoxX(), oldboxx + 5);
+ mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
+ od.getBoxY() + od.getBoxHeight() / 2 + 3);
+ assertEquals(od.getBoxX(), oldboxx + 6);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(od.getBoxY(), oldboxy + 2);
+ assertEquals(od.getBoxY(), oldboxy + 3);
assertEquals(
vpranges.getStartSeq(),
Math.round((float) od.getBoxY() * alheight
assertEquals(vpranges.getStartRes(), 0);
// click to right of hidden columns, box moves to click point
- testBoxIsAtClickPoint(40, 0);
+ mouseClick(od, 60 + boxWidth / 2, boxHeight / 2);
+ assertEquals(od.getBoxX(), 60);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(),
- Math.round((float) 40 * alwidth / od.getWidth())
+ Math.round(
+ (float) 60 * alwidth / od.getWidth())
- (lastHiddenCol + 1));
// click to right of hidden columns such that box runs over right hand side
// box position is adjusted away from the edge
// overly large boxX value reset to width-boxWidth
xpos = 100;
- mouseClick(od, xpos, 5);
+ mouseClick(od, xpos + boxWidth / 2, 5 + boxHeight / 2);
assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
assertEquals(od.getBoxY(), 5);
assertEquals(od.getBoxWidth(), boxWidth);
// move box so that it overlaps with hidden cols on one side
// box width changes, boxX and scrollCol as for unhidden case
- int xpos = 55 - boxWidth; // 55 is position in overview approx halfway
+ int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
// between cols 60 and 70
- mouseClick(od, xpos, 0);
- assertEquals(od.getBoxX(), xpos);
+ mouseClick(od, xpos, boxHeight / 2);
+ assertEquals(od.getBoxX(), xpos - boxWidth / 2);
assertEquals(od.getBoxY(), 0);
assertEquals(
od.getBoxWidth(),
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
- Math.round(xpos * alwidth / od.getWidth()));
+ Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth())
+ + 1); // +1 for rounding
assertEquals(vpranges.getStartSeq(), 0);
// move box so that it completely covers hidden cols
// box width changes, boxX and scrollCol as for hidden case
- xpos = 33;
+ xpos = 24 + boxWidth / 2;
mouseClick(od, xpos, 0);
- assertEquals(od.getBoxX(), xpos);
+ assertEquals(od.getBoxX(), 24);
assertEquals(od.getBoxY(), 0);
assertEquals(
od.getBoxWidth(),
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
- assertEquals(vpranges.getStartSeq(), 0);
-
- // move box so boxX is in hidden cols, box overhangs at right
- // boxX and scrollCol at left of hidden area, box width extends across
- // hidden region
- xpos = 50;
- mouseClick(od, xpos, 0);
- assertEquals(od.getBoxX(),
- Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth));
- assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
- boxWidth
- + Math.round((float) (lastHidden - firstHidden + 1)
- * od.getWidth() / alwidth));
- assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(vpranges.getStartRes(), firstHidden - 1);
+ Math.round((float) 24 * alwidth / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// move box so boxX is to right of hidden cols, but does not go beyond full
// width of alignment
// box width, boxX and scrollCol all as for non-hidden case
- xpos = 75;
- testBoxIsAtClickPoint(xpos, 0);
+ xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
+ mouseClick(od, xpos, boxHeight / 2);
+ assertEquals(od.getBoxX(), xpos - boxWidth / 2);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(),
- Math.round(xpos * alwidth / od.getWidth())
- - (lastHidden - firstHidden + 1));
+ 75 - (lastHidden - firstHidden + 1));
// move box so it goes beyond full width of alignment
// boxX, scrollCol adjusted back, box width normal
xpos = 3000;
mouseClick(od, xpos, 5);
assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
- assertEquals(od.getBoxY(), 5);
+ assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(
// click to left of hidden cols, without overlapping
// boxX, scrollCol and width as normal
- int xpos = 5;
- testBoxIsAtClickPoint(xpos, 0);
- assertEquals(vpranges.getStartSeq(), 0);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) xpos * alwidth / od.getWidth()));
+ int xpos = 30;
+ int ypos = 6;
+ testBoxIsAtClickPoint(xpos, ypos);
+ assertEquals(vpranges.getStartSeq(), Math
+ .round((float) (ypos - boxHeight / 2) * alheight
+ / od.getHeight()));
+ assertEquals(vpranges.getStartRes(), Math.round(
+ (float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
// click to left of hidden cols, with overlap
// boxX and scrollCol adjusted for hidden cols, width normal
xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
- mouseClick(od, xpos, 0);
+ mouseClick(od, xpos + boxWidth / 2, boxHeight / 2);
assertEquals(od.getBoxX(),
- Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+ Math.round((float) (firstHidden - 1)
+ * od.getWidth() / alwidth)
- boxWidth + 1);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
- Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ Math.round((float) (od.getBoxX()) * alwidth
+ / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// click in hidden cols
assertEquals(od.getBoxHeight(), boxHeight);
// click below hidden rows
- mouseClick(od, 0, 150);
+ mouseClick(od, 0, 150 + boxHeight/2);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 150);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows, so that box overlaps
- int ypos = 35; // column value in residues
- mouseClick(od, 0,
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
- assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(
- od.getBoxHeight(),
- boxHeight
- + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
- * od.getSequencesHeight() / alheight));
-
- // click so that box straddles hidden rows
- ypos = 44; // column value in residues
+ int rowpos = 35; // row value in residues
+ int centrepos = 43; // centre row
mouseClick(od, 0,
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round((float) centrepos * od.getSequencesHeight()
+ / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round(
+ (float) rowpos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(
od.getBoxHeight(),
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- // click above hidden rows
- int ypos = 40; // row 40
+ // click above hidden rows, no overlap
+ int ypos = 40 + viewHeight / 2; // top is row 40
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
- Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ Math.round((float) 40 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows so box overlaps
// boxY moved upwards, boxHeight remains same
- ypos = 497; // row 497
+ ypos = 497 + viewHeight / 2; // row 497
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxHeight(), boxHeight);
// click within hidden rows
- ypos = 505;
+ ypos = 505 + boxHeight / 2;
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxHeight(), boxHeight);
}
+ /**
+ * Test the function to determine if a point is in the overview's box or not
+ */
+ @Test(groups = { "Functional" })
+ public void testPositionInBox()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+
+ assertTrue(od.isPositionInBox(47, 6));
+ assertFalse(od.isPositionInBox(48, 6));
+ assertTrue(od.isPositionInBox(47, 9));
+ assertFalse(od.isPositionInBox(47, 10));
+
+ // hide columns in the box area
+ // extends area where a point is considered to be in the box
+ hiddenCols.hideColumns(1, 4);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+
+ assertTrue(od.isPositionInBox(47, 6));
+ assertTrue(od.isPositionInBox(48, 6));
+ assertTrue(od.isPositionInBox(47, 9));
+ assertFalse(od.isPositionInBox(47, 10));
+
+ // hide sequences in box area
+ // extends area where a point is considered to be in the box
+ hideSequences(1, 3);
+ ColumnSelection cs = new ColumnSelection();
+ hiddenCols.revealAllHiddenColumns(cs);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+ assertFalse(od.isPositionInBox(0, 0));
+ assertTrue(od.isPositionInBox(10, 9));
+ assertFalse(od.isPositionInBox(0, 9));
+ assertFalse(od.isPositionInBox(9, 0));
+ assertFalse(od.isPositionInBox(75, 20));
+
+ assertTrue(od.isPositionInBox(47, 6));
+ assertFalse(od.isPositionInBox(48, 6));
+ assertTrue(od.isPositionInBox(47, 9));
+ assertTrue(od.isPositionInBox(47, 10));
+ }
+
+ /**
+ * Test the dragging functionality
+ */
+ @Test(groups = { "Functional" })
+ public void testDragging()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+
+ // updates require an OverviewPanel to exist which it doesn't here
+ // so call setBoxPosition() as it would be called by the AlignmentPanel
+ // normally
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) right and 6 (22-16) up
+ assertEquals(od.getBoxX(), 16);
+ assertEquals(od.getBoxY(), 6);
+
+ // hide columns - box moves drag distance + hidden cols, vertically makes no
+ // difference
+ hiddenCols.hideColumns(1, 4);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) + hiddenCols right and 6 (22-16) down
+ assertEquals(od.getBoxX(),
+ 16 + Math.round((float) 4 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 6);
+
+ // hide sequences in box area
+ // makes absolutely no difference
+ hideSequences(1, 3);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+ // corner moves 16 (20-4) + hiddenCols right and 6 (22-16) + hiddenRows down
+ assertEquals(od.getBoxX(),
+ 16 + Math.round((float) 4 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(),
+ 6 + Math.round((float) 3 * od.getHeight() / alheight));
+ }
+
/*
* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
*/
}
/*
- * Test that the box is positioned with the top left corner at xpos, ypos
+ * Test that the box is positioned with the centre at xpos, ypos
* and with the original width and height
*/
private void testBoxIsAtClickPoint(int xpos, int ypos)
{
mouseClick(od, xpos, ypos);
- assertEquals(od.getBoxX(), xpos);
- assertEquals(od.getBoxY(), ypos);
+ assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
+ assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
git://source.jalview.org / jalview.git / commitdiff