X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=6dfb14fe72e32b8abffc2eea44308318ad127d70;hb=371f4bc519ea38c78f1c6f003df82769c130ac2e;hp=4e6747ee25a7b3e1716f256f70e0c0d63951c89d;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 4e6747e..6dfb14f 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -15,6 +15,8 @@ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; +import java.util.Enumeration; +import java.util.Vector; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -94,6 +96,16 @@ public class Viewport implements java.io.Serializable { private boolean _has_showFullId; /** + * Field _rightAlignIds + */ + private boolean _rightAlignIds; + + /** + * keeps track of state for field: _rightAlignIds + */ + private boolean _has_rightAlignIds; + + /** * Field _showText */ private boolean _showText; @@ -164,36 +176,6 @@ public class Viewport implements java.io.Serializable { private boolean _has_showAnnotation; /** - * Field _showConservation - */ - private boolean _showConservation; - - /** - * keeps track of state for field: _showConservation - */ - private boolean _has_showConservation; - - /** - * Field _showQuality - */ - private boolean _showQuality; - - /** - * keeps track of state for field: _showQuality - */ - private boolean _has_showQuality; - - /** - * Field _showIdentity - */ - private boolean _showIdentity; - - /** - * keeps track of state for field: _showIdentity - */ - private boolean _has_showIdentity; - - /** * Field _xpos */ private int _xpos; @@ -278,6 +260,66 @@ public class Viewport implements java.io.Serializable { */ private boolean _has_fontStyle; + /** + * Field _viewName + */ + private java.lang.String _viewName; + + /** + * Field _sequenceSetId + */ + private java.lang.String _sequenceSetId; + + /** + * Field _gatheredViews + */ + private boolean _gatheredViews; + + /** + * keeps track of state for field: _gatheredViews + */ + private boolean _has_gatheredViews; + + /** + * Field _textCol1 + */ + private int _textCol1; + + /** + * keeps track of state for field: _textCol1 + */ + private boolean _has_textCol1; + + /** + * Field _textCol2 + */ + private int _textCol2; + + /** + * keeps track of state for field: _textCol2 + */ + private boolean _has_textCol2; + + /** + * Field _textColThreshold + */ + private int _textColThreshold; + + /** + * keeps track of state for field: _textColThreshold + */ + private boolean _has_textColThreshold; + + /** + * Field _annotationColours + */ + private jalview.schemabinding.version2.AnnotationColours _annotationColours; + + /** + * Field _hiddenColumnsList + */ + private java.util.Vector _hiddenColumnsList; + //----------------/ //- Constructors -/ @@ -285,6 +327,7 @@ public class Viewport implements java.io.Serializable { public Viewport() { super(); + _hiddenColumnsList = new Vector(); } //-- jalview.schemabinding.version2.Viewport() @@ -293,6 +336,33 @@ public class Viewport implements java.io.Serializable { //-----------/ /** + * Method addHiddenColumns + * + * + * + * @param vHiddenColumns + */ + public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException + { + _hiddenColumnsList.addElement(vHiddenColumns); + } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) + + /** + * Method addHiddenColumns + * + * + * + * @param index + * @param vHiddenColumns + */ + public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException + { + _hiddenColumnsList.insertElementAt(vHiddenColumns, index); + } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) + + /** * Method deleteConsThreshold * */ @@ -329,6 +399,15 @@ public class Viewport implements java.io.Serializable { } //-- void deleteFontStyle() /** + * Method deleteGatheredViews + * + */ + public void deleteGatheredViews() + { + this._has_gatheredViews= false; + } //-- void deleteGatheredViews() + + /** * Method deleteHeight * */ @@ -365,6 +444,15 @@ public class Viewport implements java.io.Serializable { } //-- void deleteRenderGaps() /** + * Method deleteRightAlignIds + * + */ + public void deleteRightAlignIds() + { + this._has_rightAlignIds= false; + } //-- void deleteRightAlignIds() + + /** * Method deleteShowAnnotation * */ @@ -392,15 +480,6 @@ public class Viewport implements java.io.Serializable { } //-- void deleteShowColourText() /** - * Method deleteShowConservation - * - */ - public void deleteShowConservation() - { - this._has_showConservation= false; - } //-- void deleteShowConservation() - - /** * Method deleteShowFullId * */ @@ -410,24 +489,6 @@ public class Viewport implements java.io.Serializable { } //-- void deleteShowFullId() /** - * Method deleteShowIdentity - * - */ - public void deleteShowIdentity() - { - this._has_showIdentity= false; - } //-- void deleteShowIdentity() - - /** - * Method deleteShowQuality - * - */ - public void deleteShowQuality() - { - this._has_showQuality= false; - } //-- void deleteShowQuality() - - /** * Method deleteShowSequenceFeatures * */ @@ -464,6 +525,33 @@ public class Viewport implements java.io.Serializable { } //-- void deleteStartSeq() /** + * Method deleteTextCol1 + * + */ + public void deleteTextCol1() + { + this._has_textCol1= false; + } //-- void deleteTextCol1() + + /** + * Method deleteTextCol2 + * + */ + public void deleteTextCol2() + { + this._has_textCol2= false; + } //-- void deleteTextCol2() + + /** + * Method deleteTextColThreshold + * + */ + public void deleteTextColThreshold() + { + this._has_textColThreshold= false; + } //-- void deleteTextColThreshold() + + /** * Method deleteWidth * */ @@ -500,6 +588,29 @@ public class Viewport implements java.io.Serializable { } //-- void deleteYpos() /** + * Method enumerateHiddenColumns + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateHiddenColumns() + { + return _hiddenColumnsList.elements(); + } //-- java.util.Enumeration enumerateHiddenColumns() + + /** + * Returns the value of field 'annotationColours'. + * + * @return AnnotationColours + * @return the value of field 'annotationColours'. + */ + public jalview.schemabinding.version2.AnnotationColours getAnnotationColours() + { + return this._annotationColours; + } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() + + /** * Returns the value of field 'bgColour'. * * @return String @@ -566,6 +677,17 @@ public class Viewport implements java.io.Serializable { } //-- int getFontStyle() /** + * Returns the value of field 'gatheredViews'. + * + * @return boolean + * @return the value of field 'gatheredViews'. + */ + public boolean getGatheredViews() + { + return this._gatheredViews; + } //-- boolean getGatheredViews() + + /** * Returns the value of field 'height'. * * @return int @@ -577,6 +699,54 @@ public class Viewport implements java.io.Serializable { } //-- int getHeight() /** + * Method getHiddenColumns + * + * + * + * @param index + * @return HiddenColumns + */ + public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _hiddenColumnsList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index); + } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) + + /** + * Method getHiddenColumns + * + * + * + * @return HiddenColumns + */ + public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() + { + int size = _hiddenColumnsList.size(); + jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index); + } + return mArray; + } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() + + /** + * Method getHiddenColumnsCount + * + * + * + * @return int + */ + public int getHiddenColumnsCount() + { + return _hiddenColumnsList.size(); + } //-- int getHiddenColumnsCount() + + /** * Returns the value of field 'pidSelected'. * * @return boolean @@ -610,6 +780,28 @@ public class Viewport implements java.io.Serializable { } //-- boolean getRenderGaps() /** + * Returns the value of field 'rightAlignIds'. + * + * @return boolean + * @return the value of field 'rightAlignIds'. + */ + public boolean getRightAlignIds() + { + return this._rightAlignIds; + } //-- boolean getRightAlignIds() + + /** + * Returns the value of field 'sequenceSetId'. + * + * @return String + * @return the value of field 'sequenceSetId'. + */ + public java.lang.String getSequenceSetId() + { + return this._sequenceSetId; + } //-- java.lang.String getSequenceSetId() + + /** * Returns the value of field 'showAnnotation'. * * @return boolean @@ -643,17 +835,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean getShowColourText() /** - * Returns the value of field 'showConservation'. - * - * @return boolean - * @return the value of field 'showConservation'. - */ - public boolean getShowConservation() - { - return this._showConservation; - } //-- boolean getShowConservation() - - /** * Returns the value of field 'showFullId'. * * @return boolean @@ -665,28 +846,6 @@ public class Viewport implements java.io.Serializable { } //-- boolean getShowFullId() /** - * Returns the value of field 'showIdentity'. - * - * @return boolean - * @return the value of field 'showIdentity'. - */ - public boolean getShowIdentity() - { - return this._showIdentity; - } //-- boolean getShowIdentity() - - /** - * Returns the value of field 'showQuality'. - * - * @return boolean - * @return the value of field 'showQuality'. - */ - public boolean getShowQuality() - { - return this._showQuality; - } //-- boolean getShowQuality() - - /** * Returns the value of field 'showSequenceFeatures'. * * @return boolean @@ -731,6 +890,39 @@ public class Viewport implements java.io.Serializable { } //-- int getStartSeq() /** + * Returns the value of field 'textCol1'. + * + * @return int + * @return the value of field 'textCol1'. + */ + public int getTextCol1() + { + return this._textCol1; + } //-- int getTextCol1() + + /** + * Returns the value of field 'textCol2'. + * + * @return int + * @return the value of field 'textCol2'. + */ + public int getTextCol2() + { + return this._textCol2; + } //-- int getTextCol2() + + /** + * Returns the value of field 'textColThreshold'. + * + * @return int + * @return the value of field 'textColThreshold'. + */ + public int getTextColThreshold() + { + return this._textColThreshold; + } //-- int getTextColThreshold() + + /** * Returns the value of field 'title'. * * @return String @@ -742,6 +934,17 @@ public class Viewport implements java.io.Serializable { } //-- java.lang.String getTitle() /** + * Returns the value of field 'viewName'. + * + * @return String + * @return the value of field 'viewName'. + */ + public java.lang.String getViewName() + { + return this._viewName; + } //-- java.lang.String getViewName() + + /** * Returns the value of field 'width'. * * @return int @@ -834,6 +1037,18 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasFontStyle() /** + * Method hasGatheredViews + * + * + * + * @return boolean + */ + public boolean hasGatheredViews() + { + return this._has_gatheredViews; + } //-- boolean hasGatheredViews() + + /** * Method hasHeight * * @@ -882,6 +1097,18 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasRenderGaps() /** + * Method hasRightAlignIds + * + * + * + * @return boolean + */ + public boolean hasRightAlignIds() + { + return this._has_rightAlignIds; + } //-- boolean hasRightAlignIds() + + /** * Method hasShowAnnotation * * @@ -918,100 +1145,100 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasShowColourText() /** - * Method hasShowConservation + * Method hasShowFullId * * * * @return boolean */ - public boolean hasShowConservation() + public boolean hasShowFullId() { - return this._has_showConservation; - } //-- boolean hasShowConservation() + return this._has_showFullId; + } //-- boolean hasShowFullId() /** - * Method hasShowFullId + * Method hasShowSequenceFeatures * * * * @return boolean */ - public boolean hasShowFullId() + public boolean hasShowSequenceFeatures() { - return this._has_showFullId; - } //-- boolean hasShowFullId() + return this._has_showSequenceFeatures; + } //-- boolean hasShowSequenceFeatures() /** - * Method hasShowIdentity + * Method hasShowText * * * * @return boolean */ - public boolean hasShowIdentity() + public boolean hasShowText() { - return this._has_showIdentity; - } //-- boolean hasShowIdentity() + return this._has_showText; + } //-- boolean hasShowText() /** - * Method hasShowQuality + * Method hasStartRes * * * * @return boolean */ - public boolean hasShowQuality() + public boolean hasStartRes() { - return this._has_showQuality; - } //-- boolean hasShowQuality() + return this._has_startRes; + } //-- boolean hasStartRes() /** - * Method hasShowSequenceFeatures + * Method hasStartSeq * * * * @return boolean */ - public boolean hasShowSequenceFeatures() + public boolean hasStartSeq() { - return this._has_showSequenceFeatures; - } //-- boolean hasShowSequenceFeatures() + return this._has_startSeq; + } //-- boolean hasStartSeq() /** - * Method hasShowText + * Method hasTextCol1 * * * * @return boolean */ - public boolean hasShowText() + public boolean hasTextCol1() { - return this._has_showText; - } //-- boolean hasShowText() + return this._has_textCol1; + } //-- boolean hasTextCol1() /** - * Method hasStartRes + * Method hasTextCol2 * * * * @return boolean */ - public boolean hasStartRes() + public boolean hasTextCol2() { - return this._has_startRes; - } //-- boolean hasStartRes() + return this._has_textCol2; + } //-- boolean hasTextCol2() /** - * Method hasStartSeq + * Method hasTextColThreshold * * * * @return boolean */ - public boolean hasStartSeq() + public boolean hasTextColThreshold() { - return this._has_startSeq; - } //-- boolean hasStartSeq() + return this._has_textColThreshold; + } //-- boolean hasTextColThreshold() /** * Method hasWidth @@ -1108,6 +1335,41 @@ public class Viewport implements java.io.Serializable { } //-- void marshal(org.xml.sax.ContentHandler) /** + * Method removeAllHiddenColumns + * + */ + public void removeAllHiddenColumns() + { + _hiddenColumnsList.removeAllElements(); + } //-- void removeAllHiddenColumns() + + /** + * Method removeHiddenColumns + * + * + * + * @param index + * @return HiddenColumns + */ + public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index) + { + java.lang.Object obj = _hiddenColumnsList.elementAt(index); + _hiddenColumnsList.removeElementAt(index); + return (jalview.schemabinding.version2.HiddenColumns) obj; + } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) + + /** + * Sets the value of field 'annotationColours'. + * + * @param annotationColours the value of field + * 'annotationColours'. + */ + public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours) + { + this._annotationColours = annotationColours; + } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) + + /** * Sets the value of field 'bgColour'. * * @param bgColour the value of field 'bgColour'. @@ -1173,6 +1435,17 @@ public class Viewport implements java.io.Serializable { } //-- void setFontStyle(int) /** + * Sets the value of field 'gatheredViews'. + * + * @param gatheredViews the value of field 'gatheredViews'. + */ + public void setGatheredViews(boolean gatheredViews) + { + this._gatheredViews = gatheredViews; + this._has_gatheredViews = true; + } //-- void setGatheredViews(boolean) + + /** * Sets the value of field 'height'. * * @param height the value of field 'height'. @@ -1184,6 +1457,40 @@ public class Viewport implements java.io.Serializable { } //-- void setHeight(int) /** + * Method setHiddenColumns + * + * + * + * @param index + * @param vHiddenColumns + */ + public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _hiddenColumnsList.size())) { + throw new IndexOutOfBoundsException(); + } + _hiddenColumnsList.setElementAt(vHiddenColumns, index); + } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) + + /** + * Method setHiddenColumns + * + * + * + * @param hiddenColumnsArray + */ + public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray) + { + //-- copy array + _hiddenColumnsList.removeAllElements(); + for (int i = 0; i < hiddenColumnsArray.length; i++) { + _hiddenColumnsList.addElement(hiddenColumnsArray[i]); + } + } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) + + /** * Sets the value of field 'pidSelected'. * * @param pidSelected the value of field 'pidSelected'. @@ -1217,6 +1524,27 @@ public class Viewport implements java.io.Serializable { } //-- void setRenderGaps(boolean) /** + * Sets the value of field 'rightAlignIds'. + * + * @param rightAlignIds the value of field 'rightAlignIds'. + */ + public void setRightAlignIds(boolean rightAlignIds) + { + this._rightAlignIds = rightAlignIds; + this._has_rightAlignIds = true; + } //-- void setRightAlignIds(boolean) + + /** + * Sets the value of field 'sequenceSetId'. + * + * @param sequenceSetId the value of field 'sequenceSetId'. + */ + public void setSequenceSetId(java.lang.String sequenceSetId) + { + this._sequenceSetId = sequenceSetId; + } //-- void setSequenceSetId(java.lang.String) + + /** * Sets the value of field 'showAnnotation'. * * @param showAnnotation the value of field 'showAnnotation'. @@ -1250,17 +1578,6 @@ public class Viewport implements java.io.Serializable { } //-- void setShowColourText(boolean) /** - * Sets the value of field 'showConservation'. - * - * @param showConservation the value of field 'showConservation' - */ - public void setShowConservation(boolean showConservation) - { - this._showConservation = showConservation; - this._has_showConservation = true; - } //-- void setShowConservation(boolean) - - /** * Sets the value of field 'showFullId'. * * @param showFullId the value of field 'showFullId'. @@ -1272,28 +1589,6 @@ public class Viewport implements java.io.Serializable { } //-- void setShowFullId(boolean) /** - * Sets the value of field 'showIdentity'. - * - * @param showIdentity the value of field 'showIdentity'. - */ - public void setShowIdentity(boolean showIdentity) - { - this._showIdentity = showIdentity; - this._has_showIdentity = true; - } //-- void setShowIdentity(boolean) - - /** - * Sets the value of field 'showQuality'. - * - * @param showQuality the value of field 'showQuality'. - */ - public void setShowQuality(boolean showQuality) - { - this._showQuality = showQuality; - this._has_showQuality = true; - } //-- void setShowQuality(boolean) - - /** * Sets the value of field 'showSequenceFeatures'. * * @param showSequenceFeatures the value of field @@ -1339,6 +1634,39 @@ public class Viewport implements java.io.Serializable { } //-- void setStartSeq(int) /** + * Sets the value of field 'textCol1'. + * + * @param textCol1 the value of field 'textCol1'. + */ + public void setTextCol1(int textCol1) + { + this._textCol1 = textCol1; + this._has_textCol1 = true; + } //-- void setTextCol1(int) + + /** + * Sets the value of field 'textCol2'. + * + * @param textCol2 the value of field 'textCol2'. + */ + public void setTextCol2(int textCol2) + { + this._textCol2 = textCol2; + this._has_textCol2 = true; + } //-- void setTextCol2(int) + + /** + * Sets the value of field 'textColThreshold'. + * + * @param textColThreshold the value of field 'textColThreshold' + */ + public void setTextColThreshold(int textColThreshold) + { + this._textColThreshold = textColThreshold; + this._has_textColThreshold = true; + } //-- void setTextColThreshold(int) + + /** * Sets the value of field 'title'. * * @param title the value of field 'title'. @@ -1349,6 +1677,16 @@ public class Viewport implements java.io.Serializable { } //-- void setTitle(java.lang.String) /** + * Sets the value of field 'viewName'. + * + * @param viewName the value of field 'viewName'. + */ + public void setViewName(java.lang.String viewName) + { + this._viewName = viewName; + } //-- void setViewName(java.lang.String) + + /** * Sets the value of field 'width'. * * @param width the value of field 'width'.