public interface AlignViewportI extends ViewStyleI
{
- int getCharWidth();
-
int getEndRes();
- int getCharHeight();
-
/**
* calculate the height for visible annotation, revalidating bounds where
* necessary ABSTRACT GUI METHOD
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
- /**
- * @return true if a reference sequence is set and should be displayed
- */
- public boolean isDisplayReferenceSeq();
-
- /**
- * @return set the flag for displaying reference sequences when they are
- * available
- */
- public void setDisplayReferenceSeq(boolean displayReferenceSeq);
-
- /**
- * @return true if colourschemes should render according to reference sequence
- * rather than consensus if available
- */
- public boolean isColourByReferenceSeq();
-
- /**
- * @return true set flag for deciding if colourschemes should render according
- * to reference sequence rather than consensus if available
- */
- public void setColourByReferenceSeq(boolean colourByReferenceSeq);
-
void setSequenceColour(SequenceI seq, Color col);
Color getSequenceColour(SequenceI seq);
String getSequenceSetId();
- boolean isShowSequenceFeatures();
-
- void setShowSequenceFeatures(boolean b);
-
- /**
- *
- * @param flag
- * indicating if annotation panel shown below alignment
- *
- */
- void setShowAnnotation(boolean b);
-
- /**
- * flag indicating if annotation panel shown below alignment
- *
- * @return
- */
- boolean isShowAnnotation();
-
- boolean isRightAlignIds();
-
- void setRightAlignIds(boolean rightAlignIds);
-
boolean areFeaturesDisplayed();
- void setShowSequenceFeaturesHeight(boolean selected);
-
- boolean isShowSequenceFeaturesHeight();
-
void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
void alignmentChanged(AlignmentViewPanel ap);
void setShowUnconserved(boolean showunconserved);
+ /**
+ * @return true if a reference sequence is set and should be displayed
+ */
boolean isDisplayReferenceSeq();
+ /**
+ * @return set the flag for displaying reference sequences when they are
+ * available
+ */
void setDisplayReferenceSeq(boolean displayReferenceSeq);
+ /**
+ * @return true if colourschemes should render according to reference sequence
+ * rather than consensus if available
+ */
boolean isColourByReferenceSeq();
void setSeqNameItalics(boolean default1);
void setRightAlignIds(boolean rightAlignIds);
+ /**
+ * Returns true if annotation panel should be shown below alignment
+ *
+ * @return
+ */
boolean isShowAnnotation();
+ /**
+ * Set flag for whether annotation panel should be shown below alignment
+ *
+ * @param b
+ */
void setShowAnnotation(boolean b);
- void setShowSeqFeaturesHeight(boolean selected);
-
- boolean isShowSequenceFeaturesHeight();
+ void setShowSequenceFeaturesHeight(boolean selected);
+ /**
+ * @return true set flag for deciding if colourschemes should render according
+ * to reference sequence rather than consensus if available
+ */
void setColourByReferenceSeq(boolean colourByReferenceSeq);
Color getTextColour();
boolean isShowColourText();
- boolean isShowSeqFeaturesHeight();
+ boolean isShowSequenceFeaturesHeight();
void setConservationColourSelected(boolean conservationColourSelected);
import jalview.viewmodel.AlignmentViewport;
public class AlignViewport extends AlignmentViewport implements
- AlignViewportI, SelectionSource, VamsasSource, CommandListener
+ SelectionSource, VamsasSource, CommandListener
{
boolean cursorMode = false;
String file = "No file";
- String file2 = "No file";
+ String file2 = null;
Button launcher = new Button(
MessageManager.getString("label.start_jalview"));
file = data.toString();
}
}
- if ("true".equalsIgnoreCase(getParameter("enableSplitFrame")))
+ if (TRUE.equalsIgnoreCase(getParameter("enableSplitFrame")))
{
file2 = getParameter("file2");
}
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, AlignViewportI, CommandListener
+ SelectionSource, CommandListener
{
Font font;
*
*/
public abstract class AlignmentViewport implements AlignViewportI,
- ViewStyleI, CommandListener, VamsasSource
+ CommandListener, VamsasSource
{
protected ViewStyleI viewStyle = new ViewStyle();
}
/**
- * @param selected
- * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
- */
- public void setShowSeqFeaturesHeight(boolean selected)
- {
- viewStyle.setShowSeqFeaturesHeight(selected);
- }
-
- /**
* alignment displayed in the viewport. Please use get/setter
*/
protected AlignmentI alignment;
@Override
public void setShowSequenceFeaturesHeight(boolean selected)
{
- viewStyle.setShowSeqFeaturesHeight(selected);
+ viewStyle.setShowSequenceFeaturesHeight(selected);
}
@Override
{
return viewStyle.isShowColourText();
}
- /**
- * @return
- * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
- */
- public boolean isShowSeqFeaturesHeight()
- {
- return viewStyle.isShowSeqFeaturesHeight();
- }
/**
* @param conservationColourSelected
package jalview.viewmodel.styles;
import java.awt.Color;
-import java.lang.reflect.Method;
-import java.util.HashMap;
import jalview.api.ViewStyleI;
*/
public class ViewStyle implements ViewStyleI
{
-
private boolean abovePIDThreshold = false;
int charHeight;
*/
private boolean scaleProteinAsCdna = true;
- public ViewStyle(ViewStyleI viewStyle)
- {
- ViewStyle.configureFrom(this, viewStyle);
+ /**
+ * Copy constructor
+ *
+ * @param vs
+ */
+ public ViewStyle(ViewStyleI vs)
+ {
+ setAbovePIDThreshold(vs.getAbovePIDThreshold());
+ setCentreColumnLabels(vs.isCentreColumnLabels());
+ setCharHeight(vs.getCharHeight());
+ setCharWidth(vs.getCharWidth());
+ setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups());
+ setColourByReferenceSeq(vs.isColourByReferenceSeq());
+ setColourText(vs.getColourText());
+ setConservationColourSelected(vs.isConservationColourSelected());
+ setConservationSelected(vs.getConservationSelected());
+ setDisplayReferenceSeq(vs.isDisplayReferenceSeq());
+ setFontName(vs.getFontName());
+ setFontSize(vs.getFontSize());
+ setFontStyle(vs.getFontStyle());
+ setIdWidth(vs.getIdWidth());
+ setIncrement(vs.getIncrement());
+ setRenderGaps(vs.isRenderGaps());
+ setRightAlignIds(vs.isRightAlignIds());
+ setScaleAboveWrapped(vs.getScaleAboveWrapped());
+ setScaleLeftWrapped(vs.getScaleLeftWrapped());
+ setScaleProteinAsCdna(vs.isScaleProteinAsCdna());
+ setScaleRightWrapped(vs.getScaleRightWrapped());
+ setSeqNameItalics(vs.isSeqNameItalics());
+ setShowAnnotation(vs.isShowAnnotation());
+ setShowBoxes(vs.getShowBoxes());
+ setShowColourText(vs.isShowColourText());
+ setShowDBRefs(vs.isShowDBRefs());
+ setShowHiddenMarkers(vs.getShowHiddenMarkers());
+ setShowJVSuffix(vs.getShowJVSuffix());
+ setShowNPFeats(vs.isShowNPFeats());
+ setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight());
+ setShowSequenceFeatures(vs.isShowSequenceFeatures());
+ setShowText(vs.getShowText());
+ setShowUnconserved(vs.getShowUnconserved());
+ setTextColour(vs.getTextColour());
+ setTextColour2(vs.getTextColour2());
+ setThreshold(vs.getThreshold());
+ setThresholdTextColour(vs.getThresholdTextColour());
+ setUpperCasebold(vs.isUpperCasebold());
+ setWrapAlignment(vs.getWrapAlignment());
+ setWrappedWidth(vs.getWrappedWidth());
+ // ViewStyle.configureFrom(this, viewStyle);
}
public ViewStyle()
{
}
- private static HashMap<String, Method> getters, isErs, setters;
- static
+ /**
+ * Returns true if all attributes of the ViewStyles have the same value
+ */
+ @Override
+ public boolean equals(Object other)
{
- getters = new HashMap<String, Method>();
- isErs = new HashMap<String, Method>();
- setters = new HashMap<String, Method>();
- // Match Getters and Setters
- for (Method m : ViewStyleI.class.getMethods())
- {
- if (m.getDeclaringClass() == ViewStyleI.class)
- {
- if (m.getName().startsWith("get"))
- {
- getters.put(m.getName().substring(3), m);
- }
- if (m.getName().startsWith("is"))
- {
- isErs.put(m.getName().substring(2), m);
- }
- if (m.getName().startsWith("set"))
- {
- setters.put(m.getName().substring(3), m);
- }
- }
- }
- }
-
- private static void configureFrom(ViewStyle us, ViewStyleI viewStyle)
- {
- // try and do the set thing
- for (String prop : setters.keySet())
- {
- Method getter = getters.get(prop);
- Method setter = setters.get(prop);
- if (getter == null)
- {
- getter = isErs.get(prop);
- }
- if (getter != null && setter != null)
- {
- try
- {
- setter.invoke(us, getter.invoke(viewStyle));
- } catch (Exception q)
- {
- System.err.println("Unexpected exception setting view property "
- + prop + " by reflection");
- q.printStackTrace();
- }
-
- }
- }
- }
-
- private static boolean equivalent(ViewStyle us, ViewStyleI them)
- {
- // look for properties we can set
- for (String prop : setters.keySet())
+ if (other == null || !(other instanceof ViewStyle))
{
- Method getter = getters.get(prop);
- if (getter == null)
- {
- getter = isErs.get(prop);
- }
- if (getter != null)
- {
- try
- {
- if (!getter.invoke(them).equals(getter.invoke(us)))
- {
- return false;
- }
- } catch (Exception q)
- {
- System.err.println("Unexpected exception testing equivalence of property "
- + prop + " by reflection");
- q.printStackTrace();
- }
- }
+ return false;
}
-
- return true;
+ ViewStyle vs = (ViewStyle) other;
+
+ boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold()
+ && isCentreColumnLabels() == vs.isCentreColumnLabels()
+ && getCharHeight() == vs.getCharHeight()
+ && getCharWidth() == vs.getCharWidth()
+ && getColourAppliesToAllGroups() == vs
+ .getColourAppliesToAllGroups()
+ && isColourByReferenceSeq() == vs.isColourByReferenceSeq()
+ && getColourText() == vs.getColourText()
+ && isConservationColourSelected() == vs
+ .isConservationColourSelected()
+ && getConservationSelected() == vs.getConservationSelected()
+ && isDisplayReferenceSeq() == vs.isDisplayReferenceSeq()
+ && getFontSize() == vs.getFontSize()
+ && getFontStyle() == vs.getFontStyle()
+ && getIdWidth() == vs.getIdWidth()
+ && getIncrement() == vs.getIncrement()
+ && isRenderGaps() == vs.isRenderGaps()
+ && isRightAlignIds() == vs.isRightAlignIds()
+ && getScaleAboveWrapped() == vs.getScaleAboveWrapped()
+ && getScaleLeftWrapped() == vs.getScaleLeftWrapped()
+ && isScaleProteinAsCdna() == vs.isScaleProteinAsCdna()
+ && getScaleRightWrapped() == vs.getScaleRightWrapped()
+ && isSeqNameItalics() == vs.isSeqNameItalics()
+ && isShowAnnotation() == vs.isShowAnnotation()
+ && getShowBoxes() == vs.getShowBoxes()
+ && isShowColourText() == vs.isShowColourText()
+ && isShowDBRefs() == vs.isShowDBRefs()
+ && getShowHiddenMarkers() == vs.getShowHiddenMarkers()
+ && getShowJVSuffix() == vs.getShowJVSuffix()
+ && isShowNPFeats() == vs.isShowNPFeats()
+ && isShowSequenceFeaturesHeight() == vs
+ .isShowSequenceFeaturesHeight()
+ && isShowSequenceFeatures() == vs.isShowSequenceFeatures()
+ && getShowText() == vs.getShowText()
+ && getShowUnconserved() == vs.getShowUnconserved()
+ && getThreshold() == vs.getThreshold()
+ && getThresholdTextColour() == vs.getThresholdTextColour()
+ && isUpperCasebold() == vs.isUpperCasebold()
+ && getWrapAlignment() == vs.getWrapAlignment() && getWrappedWidth() == vs
+ .getWrappedWidth());
+ /*
+ * and compare non-primitive types; syntax below will match null with null values
+ */
+ match = match
+ && String.valueOf(getFontName()).equals(
+ String.valueOf(vs.getFontName()));
+ match = match
+ && String.valueOf(getTextColour()).equals(
+ String.valueOf(vs.getTextColour()));
+ match = match
+ && String.valueOf(getTextColour2()).equals(
+ String.valueOf(vs.getTextColour2()));
+ return match;
+ // return equivalent(this, (ViewStyle) other);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return 0; // TODO
}
-
- public boolean equals(ViewStyleI other)
- {
- return other == null ? false : equivalent(this, other);
- }
-
/**
* @return the upperCasebold
*/
* @return the showSeqFeaturesHeight
*/
@Override
- public boolean isShowSeqFeaturesHeight()
+ public boolean isShowSequenceFeaturesHeight()
{
return showSeqFeaturesHeight;
}
return showSequenceFeatures;
}
- @Override
- public boolean isShowSequenceFeaturesHeight()
- {
-
- return showSeqFeaturesHeight;
- }
-
/**
* GUI state
*
}
@Override
- public void setShowSeqFeaturesHeight(boolean selected)
+ public void setShowSequenceFeaturesHeight(boolean selected)
{
showSeqFeaturesHeight = selected;
}
@Override
- public boolean sameStyle(ViewStyleI them)
+ public boolean sameStyle(ViewStyleI that)
{
- return equivalent(this, them);
+ return this.equals(that);
}
@Override
+++ /dev/null
-package jalview.viewmodel.styles;
-
-import org.junit.Assert;
-import org.junit.Test;
-
-public class TestviewStyle
-{
-
- @Test
- public void testSetterGetter()
- {
- ViewStyle orig = new ViewStyle();
- orig.setCharHeight(23);
- orig.setWrappedWidth(253);
- orig.setWrapAlignment(true);
- orig.setScaleProteinAsCdna(true);
-
- ViewStyle copy = new ViewStyle(orig);
- orig.setWrapAlignment(false);
- Assert.assertEquals(copy.getCharHeight(), orig.getCharHeight());
- Assert.assertEquals(copy.getWrappedWidth(), orig.getWrappedWidth());
- Assert.assertEquals(copy.getWrapAlignment(), !orig.getWrapAlignment());
- Assert.assertEquals(copy.isScaleProteinAsCdna(),
- orig.isScaleProteinAsCdna());
- }
-
-}
--- /dev/null
+package jalview.viewmodel.styles;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.lang.reflect.Field;
+import java.util.Random;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+
+public class ViewStyleTest
+{
+
+ Random r = new Random();
+
+ /**
+ * This test uses reflection to set all fields on a ViewStyle, make a copy of
+ * it, and verify all fields match. This test should fail if a getter/setter
+ * pair are added to the class but missing in the copy constructor. Using
+ * reflection in the copy constructor itself is broken by obfuscation when the
+ * applet is built.
+ *
+ * To prove this test works, simply comment out a line in the ViewStyle copy
+ * constructor, or add a new member field to ViewStyle.
+ *
+ * @throws IllegalAccessException
+ * @throws IllegalArgumentException
+ */
+ @Test
+ public void testCopyConstructor() throws IllegalArgumentException,
+ IllegalAccessException
+ {
+ ViewStyle vs1 = new ViewStyle();
+ Field[] fields = ViewStyle.class.getDeclaredFields();
+ for (Field field : fields)
+ {
+ field.setAccessible(true);
+ changeValue(vs1, field);
+ }
+
+ ViewStyle vs2 = new ViewStyle(vs1);
+
+ for (Field field1 : fields) {
+ final Object value1 = field1.get(vs1);
+ final Object value2 = field1.get(vs2);
+ String msg = "Mismatch in " + field1.getName() + "(" + value1 + "/"
+ + value2 + ") - not set in copy constructor?";
+ assertEquals(msg, value1, value2);
+ }
+ }
+
+ /**
+ * Change the value of one field in a ViewStyle object
+ *
+ * @param vs
+ * @param field
+ * @throws IllegalAccessException
+ */
+ protected void changeValue(ViewStyle vs, Field field)
+ throws IllegalAccessException
+ {
+ Class<?> type = field.getType();
+ final int numValue = 1 + r.nextInt(100);
+
+ if (type.equals(boolean.class) || type.equals(Boolean.class))
+ {
+ boolean value = (Boolean) field.get(vs);
+ // System.out.println("Setting " + field.getName() + " to " + !value);
+ field.set(vs, !value);
+ }
+ else if (type.equals(short.class) || type.equals(int.class)
+ || type.equals(long.class) || type.equals(float.class)
+ || type.equals(double.class))
+ {
+ final int value = (int) (1 + field.getDouble(vs));
+ // System.out.println("Setting " + field.getName() + " to " + value);
+ field.set(vs, value);
+ }
+ else if (type.equals(Integer.class))
+ {
+ field.set(vs, (int) (1 + getNumberValue(field, vs)));
+ }
+ else if (type.equals(Float.class))
+ {
+ field.set(vs, (float) (1f + getNumberValue(field, vs)));
+ }
+ else if (type.equals(Long.class))
+ {
+ field.set(vs, (long) (1L + getNumberValue(field, vs)));
+ }
+ else if (type.equals(Double.class))
+ {
+ field.set(vs, 1d + getNumberValue(field, vs));
+ }
+ else if (type.equals(Short.class))
+ {
+ field.set(vs, (short) (1 + getNumberValue(field, vs)));
+ }
+ else if (type.equals(Byte.class))
+ {
+ field.set(vs, (byte) (1 + getNumberValue(field, vs)));
+ }
+ else if (type.equals(Character.class))
+ {
+ field.set(vs, (char) (1 + getNumberValue(field, vs)));
+ }
+ else if (type.equals(String.class))
+ {
+ field.set(vs, "Joe" + field.get(vs));
+ }
+ else if (type.equals(Color.class))
+ {
+ field.set(vs, Color.RED.equals(field.get(vs)) ? Color.BLACK
+ : Color.RED);
+ }
+ else
+ {
+ Assert.fail("Unhandled field type (add to test): " + field.getName()
+ + ":" + type);
+ }
+ }
+
+ private double getNumberValue(Field field, ViewStyle vs)
+ throws IllegalArgumentException, IllegalAccessException
+ {
+ if (field.get(vs) == null)
+ {
+ return 0d;
+ }
+ return ((Number) field.get(vs)).doubleValue();
+ }
+
+ /**
+ * Test that the equals method compares every field by changing them one by
+ * one in a cloned ViewStyle.
+ *
+ * This test will fail if a new field is added to ViewStyle but not to the
+ * comparisons in ViewStyle.equals().
+ *
+ * To confirm that this test works, temporarily comment out one of the field
+ * comparisons in ViewStyle.equals()
+ *
+ * @throws IllegalAccessException
+ * @throws IllegalArgumentException
+ */
+ @Test
+ public void testEquals() throws IllegalArgumentException,
+ IllegalAccessException
+ {
+ ViewStyle vs1 = new ViewStyle();
+ ViewStyle vs2 = new ViewStyle(vs1);
+
+ assertFalse(vs1.equals(null));
+ assertFalse(vs1.equals(this));
+ assertTrue(vs1.equals(vs2));
+ assertTrue(vs2.equals(vs1));
+
+ Field[] fields = ViewStyle.class.getDeclaredFields();
+ for (Field field : fields)
+ {
+ field.setAccessible(true);
+ Object oldValue = field.get(vs2);
+ changeValue(vs2, field);
+ assertFalse("equals method ignores " + field.getName(),
+ vs1.equals(vs2));
+ // restore original value before testing the next field
+ field.set(vs2, oldValue);
+ }
+ }
+}
git://source.jalview.org / jalview.git / commitdiff