diff --git a/uk/ac/sanger/artemis/AlignMatchVector.java b/uk/ac/sanger/artemis/AlignMatchVector.java index 3357a0356809ae1a5dff095dc69e4c52a0a4c6b3..de26c6d054a3a01c97b2eb1e272669c9a3f4d1e2 100644 --- a/uk/ac/sanger/artemis/AlignMatchVector.java +++ b/uk/ac/sanger/artemis/AlignMatchVector.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/AlignMatchVector.java,v 1.1 2004-06-09 09:44:07 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/AlignMatchVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis; @@ -34,7 +34,7 @@ import java.util.Collections; * This class is a Vector of AlignMatch objects. * * @author Kim Rutherford <kmr@sanger.ac.uk> - * @version $Id: AlignMatchVector.java,v 1.1 2004-06-09 09:44:07 tjc Exp $ + * @version $Id: AlignMatchVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ **/ public class AlignMatchVector { @@ -65,7 +65,7 @@ public class AlignMatchVector { * Performs the same function as Vector.elementAt () **/ public AlignMatch elementAt (int index) { - return (AlignMatch) vector.elementAt (index); + return (AlignMatch) vector.get(index); } /** @@ -90,7 +90,7 @@ public class AlignMatchVector { * Performs the same function as Vector.removeAllElements () **/ public void removeAllElements () { - vector.removeAllElements (); + vector.clear (); } /** diff --git a/uk/ac/sanger/artemis/FeatureSegmentVector.java b/uk/ac/sanger/artemis/FeatureSegmentVector.java index e9956e68367d6d425aa93694e23837aa8068ac1a..68765ea951d3978b9cfa34dc657b5de1c9c4f46f 100644 --- a/uk/ac/sanger/artemis/FeatureSegmentVector.java +++ b/uk/ac/sanger/artemis/FeatureSegmentVector.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/FeatureSegmentVector.java,v 1.1 2004-06-09 09:44:48 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/FeatureSegmentVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis; @@ -31,7 +31,7 @@ import uk.ac.sanger.artemis.util.FastVector; * This class implements a Vector of FeatureSegment objects. * * @author Kim Rutherford - * @version $Id: FeatureSegmentVector.java,v 1.1 2004-06-09 09:44:48 tjc Exp $ + * @version $Id: FeatureSegmentVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ * **/ @@ -61,7 +61,7 @@ public class FeatureSegmentVector { * Performs the same function as Vector.insertElementAt () **/ public void insertElementAt (FeatureSegment segment, int index) { - vector.insertElementAt (segment, index); + vector.add (index, segment); } /** @@ -75,14 +75,14 @@ public class FeatureSegmentVector { * Performs the same function as Vector.elementAt () **/ public FeatureSegment elementAt (int index) { - return (FeatureSegment) vector.elementAt (index); + return (FeatureSegment) vector.get(index); } /** * Performs the same function as Vector.lastElement () **/ public FeatureSegment lastElement () { - return (FeatureSegment) vector.lastElement (); + return (FeatureSegment) vector.lastElement(); } /** @@ -114,14 +114,14 @@ public class FeatureSegmentVector { * Performs the same function as Vector.removeAllElement () **/ public void removeAllElements () { - vector.removeAllElements (); + vector.clear (); } /** * Performs the same function as Vector.removeElementAt () **/ public void removeElementAt (int index) { - vector.removeElementAt (index); + vector.remove (index); } /** @@ -135,7 +135,7 @@ public class FeatureSegmentVector { * Add a feature to the end of the Vector. **/ public void addElementAtEnd (FeatureSegment segment) { - vector.insertElementAt (segment, size ()); + vector.add (size(), segment); } /** diff --git a/uk/ac/sanger/artemis/FeatureVector.java b/uk/ac/sanger/artemis/FeatureVector.java index c113240cadef31f60fc5b4d3c7e36012775d3b94..99ae0deb4d382d5416f3f2471410948a13d6cc18 100644 --- a/uk/ac/sanger/artemis/FeatureVector.java +++ b/uk/ac/sanger/artemis/FeatureVector.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/FeatureVector.java,v 1.1 2004-06-09 09:44:49 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/FeatureVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis; @@ -33,7 +33,7 @@ import java.util.*; * This class implements a Vector of Feature objects. * * @author Kim Rutherford - * @version $Id: FeatureVector.java,v 1.1 2004-06-09 09:44:49 tjc Exp $ + * @version $Id: FeatureVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ * **/ @@ -63,7 +63,7 @@ public class FeatureVector { * Performs the same function as Vector.elementAt () */ public Feature elementAt (int index) { - return (Feature) vector.elementAt (index); + return (Feature) vector.get(index); } /** @@ -105,21 +105,21 @@ public class FeatureVector { * Performs the same function as Vector.removeAllElement () **/ public void removeAllElements () { - vector.removeAllElements (); + vector.clear (); } /** * Performs the same function as Vector.removeElementAt () **/ public void removeElementAt(int index) { - vector.removeElementAt (index); + vector.remove (index); } /** * Performs the same function as Vector.insertElementAt () **/ public final void insertElementAt (Feature feature, int index) { - vector.insertElementAt (feature, index); + vector.add (index, feature); } /** diff --git a/uk/ac/sanger/artemis/components/KeyChoice.java b/uk/ac/sanger/artemis/components/KeyChoice.java index 190df9575d820b7fca04437e6114cad489d3924e..a9de6e15629fd439ea7588cbb2d47d2c3762b5ba 100644 --- a/uk/ac/sanger/artemis/components/KeyChoice.java +++ b/uk/ac/sanger/artemis/components/KeyChoice.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/KeyChoice.java,v 1.2 2005-02-17 14:18:38 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/KeyChoice.java,v 1.3 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis.components; @@ -41,7 +41,7 @@ import javax.swing.*; * This component is a Choice component that shows the possible feature keys. * * @author Kim Rutherford - * @version $Id: KeyChoice.java,v 1.2 2005-02-17 14:18:38 tjc Exp $ + * @version $Id: KeyChoice.java,v 1.3 2006-08-09 16:35:31 tjc Exp $ **/ public class KeyChoice extends JPanel { /** @@ -140,7 +140,7 @@ public class KeyChoice extends JPanel { } for (int i = 0 ; i < keys.size () ; ++i) { - key_chooser.addItem (keys.elementAt (i).toString ()); + key_chooser.addItem ( ((Key)keys.get(i)).toString ()); } if (keyIndex (default_key) != -1) { diff --git a/uk/ac/sanger/artemis/components/SelectMenu.java b/uk/ac/sanger/artemis/components/SelectMenu.java index 7f7acdc1122c006c5d4978e9fd41f3caef27d5df..7a8dcae44b3f93757ff1fa510b8d8033e2a820da 100644 --- a/uk/ac/sanger/artemis/components/SelectMenu.java +++ b/uk/ac/sanger/artemis/components/SelectMenu.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/SelectMenu.java,v 1.9 2006-01-17 16:05:05 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/SelectMenu.java,v 1.10 2006-08-09 16:35:31 tjc Exp $ **/ package uk.ac.sanger.artemis.components; @@ -50,7 +50,7 @@ import javax.swing.*; * "Select by key". * * @author Kim Rutherford - * @version $Id: SelectMenu.java,v 1.9 2006-01-17 16:05:05 tjc Exp $ + * @version $Id: SelectMenu.java,v 1.10 2006-08-09 16:35:31 tjc Exp $ **/ public class SelectMenu extends SelectionMenu @@ -643,7 +643,7 @@ public class SelectMenu extends SelectionMenu clearSelection (); for (int i = 0 ; i < seen_keys.size () ; ++i) { - selectByKey (seen_keys.elementAt (i)); + selectByKey ((Key)seen_keys.get(i)); } } diff --git a/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java b/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java index f56bb56b14c81be9c6877b4e11f3debf27bb61c0..d89ec5f5ec3219f699e01a54d0efe7d34ae4c07b 100644 --- a/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java +++ b/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java,v 1.4 2006-03-22 14:03:35 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java,v 1.5 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis.io; @@ -33,7 +33,7 @@ import java.io.*; * called #entry_name# every 120 seconds. * * @author Kim Rutherford <kmr@sanger.ac.uk> - * @version $Id: DocumentEntryAutosaveThread.java,v 1.4 2006-03-22 14:03:35 tjc Exp $ + * @version $Id: DocumentEntryAutosaveThread.java,v 1.5 2006-08-09 16:35:31 tjc Exp $ **/ public class DocumentEntryAutosaveThread extends Thread { @@ -62,9 +62,9 @@ public class DocumentEntryAutosaveThread extends Thread { boolean have_saved = false; try { - // sleep for 15 seconds before starting - there is no point in attempting + // sleep for 120 seconds before starting - there is no point in attempting // to save straight away - Thread.sleep (15000); + Thread.sleep (120000); } catch (InterruptedException _) { } diff --git a/uk/ac/sanger/artemis/io/Key.java b/uk/ac/sanger/artemis/io/Key.java index 5c4049d5a663538325f9d436f7477bedc346bb9d..7ba2741dde37bc368d52518c5f0e485bdcfef169 100644 --- a/uk/ac/sanger/artemis/io/Key.java +++ b/uk/ac/sanger/artemis/io/Key.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/Key.java,v 1.1 2004-06-09 09:49:43 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/Key.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis.io; @@ -32,7 +32,7 @@ import uk.ac.sanger.artemis.util.*; * with a limited number of possible values. * * @author Kim Rutherford - * @version $Id: Key.java,v 1.1 2004-06-09 09:49:43 tjc Exp $ + * @version $Id: Key.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ **/ public class Key @@ -88,14 +88,11 @@ public class Key public boolean equals (final Object test_object) { if(test_object instanceof String) - return getKeyString ().equals ((String) test_object); + return key_string.equals(test_object); + else if(test_object instanceof Key) + return key_string.equals (((Key) test_object).getKeyString ()); else - { - if(test_object instanceof Key) - return getKeyString ().equals (((Key) test_object).getKeyString ()); - else - return false; - } + return false; } /** diff --git a/uk/ac/sanger/artemis/io/KeyVector.java b/uk/ac/sanger/artemis/io/KeyVector.java index 45637cfc1196e2fa8f4e5f524e0e0dad44817833..95aa4555ee144967888a735b5f741b4dfcf8d2c8 100644 --- a/uk/ac/sanger/artemis/io/KeyVector.java +++ b/uk/ac/sanger/artemis/io/KeyVector.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/KeyVector.java,v 1.1 2004-06-09 09:49:45 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/KeyVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis.io; @@ -31,91 +31,32 @@ import uk.ac.sanger.artemis.util.FastVector; * This class implements a Vector of Key objects. * * @author Kim Rutherford - * @version $Id: KeyVector.java,v 1.1 2004-06-09 09:49:45 tjc Exp $ + * @version $Id: KeyVector.java,v 1.2 2006-08-09 16:35:31 tjc Exp $ **/ -public class KeyVector +public class KeyVector extends FastVector { - /** Storage for Key objects. */ - private FastVector vector; - /** - * Create a new vector of Key objects. - **/ - public KeyVector () + public KeyVector () { - vector = new FastVector (); + super(); } - + /** * Create a new vector which contains only the given Key. **/ public KeyVector (final Key new_key) { - vector = new FastVector (); + super(); add (new_key); } - /** - * Performs the same function as Vector.addElement () - **/ - public void add (final Key node) - { - vector.add (node); - } - - /** - * Performs the same function as Vector.elementAt () - **/ - public Key elementAt (final int index) - { - return (Key) vector.elementAt (index); - } - - /** - * Performs the same function as Vector.setElementAt () - **/ - public void setElementAt (final Key key, final int index) - { - vector.setElementAt (key, index); - } - - /** - * Performs the same function as Vector.size () - **/ - public int size () - { - return vector.size (); - } - - /** - * Searches for the first occurence of the given argument, testing for - * equality using the equals method. - * @return the index of the first occurrence of the argument in this - * vector; returns -1 if the object is not found. - **/ - public int indexOf (final Key key) - { - return vector.indexOf (key); - } - - /** - * Return true if this object contains the given Key, testing for - * equality using the equals method. - **/ - public boolean contains (final Key key) - { - return vector.contains (key); - } - /** * Return a new copy of this object. **/ public KeyVector copy () { - final KeyVector new_key_vector = new KeyVector (); - - new_key_vector.vector = (FastVector) vector.clone (); + final KeyVector new_key_vector = (KeyVector)clone(); return new_key_vector; } @@ -124,7 +65,7 @@ public class KeyVector * Sorts the elements of the vector using a simple O(n^2) selection * sort. */ - public void sort () + public void sort() { int smallest; @@ -134,14 +75,14 @@ public class KeyVector smallest = i; for(int j = i + 1 ; j < size () ; ++j) { - if(elementAt(j).compareTo (elementAt(smallest)) < 0) + if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0) smallest = j; } //exchange smallest and i if (smallest != i) { - final Key tmp = elementAt (i); - setElementAt (elementAt(smallest), i); + final Key tmp = (Key)get(i); + setElementAt (get(smallest), i); setElementAt (tmp, smallest); } } diff --git a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java index 21b6631c4179f9c355d7c8fabf635e8587aafd2d..749d397d72159a7700e27d166b75db58c795e62b 100644 --- a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java +++ b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleEntryInformation.java,v 1.2 2005-10-11 14:20:31 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleEntryInformation.java,v 1.3 2006-08-09 16:35:31 tjc Exp $ */ @@ -35,7 +35,7 @@ import java.util.*; * qualifier. * * @author Kim Rutherford - * @version $Id: SimpleEntryInformation.java,v 1.2 2005-10-11 14:20:31 tjc Exp $ + * @version $Id: SimpleEntryInformation.java,v 1.3 2006-08-09 16:35:31 tjc Exp $ **/ public class SimpleEntryInformation @@ -123,7 +123,7 @@ public class SimpleEntryInformation if (qualifier_valid_keys != null) { for (int i = 0 ; i < qualifier_valid_keys.size () ; ++i) { - final Key this_key = qualifier_valid_keys.elementAt (i); + final Key this_key = (Key)qualifier_valid_keys.get(i); if (valid_keys != null && valid_keys.contains (this_key)) { continue; @@ -155,8 +155,8 @@ public class SimpleEntryInformation if (user_keys != null) { for (int i = 0 ; i < user_keys.size () ; ++i) { - if (!return_keys.contains (user_keys.elementAt (i))) { - return_keys.add (user_keys.elementAt (i)); + if (!return_keys.contains ((Key)user_keys.get (i))) { + return_keys.add ((Key)user_keys.get (i)); } } } @@ -189,7 +189,7 @@ public class SimpleEntryInformation if (isValidKey (misc_feature_key)) { return misc_feature_key; } else { - return getValidKeys ().elementAt (0); + return (Key)getValidKeys ().get (0); } } @@ -395,7 +395,7 @@ public class SimpleEntryInformation return getQualifierInfoHash ().copy (); } } - + /** * Fix this EntryInformation so that the given exception won't happen * again. diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java index 96836b2b6833f33e3522559135330f89d5144e6f..f0561788420528b17148d663e91873ece8694835 100644 --- a/uk/ac/sanger/artemis/util/DatabaseDocument.java +++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java @@ -440,8 +440,9 @@ public class DatabaseDocument extends Document id_store, dao, feat.getFeatureloc(), this_buff); - progress_listener.progressMade("Read from database: " + - feat.getUniquename()); + if( i%10 == 0 || i == feature_size-1) + progress_listener.progressMade("Read from database: " + + feat.getUniquename()); } return buffers; diff --git a/uk/ac/sanger/artemis/util/FastVector.java b/uk/ac/sanger/artemis/util/FastVector.java index 10cf39278bb9315ab5213d07e0ae091e8def1e56..b9d1712f01847e670521acf00c7d91ec0d72b441 100644 --- a/uk/ac/sanger/artemis/util/FastVector.java +++ b/uk/ac/sanger/artemis/util/FastVector.java @@ -20,7 +20,7 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * - * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/util/FastVector.java,v 1.3 2004-12-21 09:55:33 tjc Exp $ + * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/util/FastVector.java,v 1.4 2006-08-09 16:35:31 tjc Exp $ */ package uk.ac.sanger.artemis.util; @@ -34,41 +34,23 @@ import java.util.Collections; * contains(). * * @author Kim Rutherford <kmr@sanger.ac.uk> - * @version $Id: FastVector.java,v 1.3 2004-12-21 09:55:33 tjc Exp $ + * @version $Id: FastVector.java,v 1.4 2006-08-09 16:35:31 tjc Exp $ * **/ -public class FastVector +public class FastVector extends ArrayList { - /** Storage for objects. */ - private ArrayList vector = new ArrayList(); - - /** - * Create a new vector of objects. - **/ - public FastVector() - { - } - /** * Performs the same function as Vector.addElement() */ - public void add(Object object) + public boolean add(Object object) { if(object == null) throw new Error("internal error - adding a null object"); else if(contains(object)) throw new Error("internal error - object added a second time"); - vector.add(object); - } - - /** - * Performs the same function as Vector.elementAt() - */ - public Object elementAt(int index) - { - return (Object)vector.get(index); + return super.add(object); } /** @@ -76,74 +58,9 @@ public class FastVector **/ public Object lastElement() { - return (Object)vector.get(vector.size() - 1); - } - - /** - * Performs the same function as Vector.removeElement() - **/ - public boolean remove(Object object) - { - if(contains(object)) - { - vector.remove(object); - return true; - } - else - return false; - } - - /** - * Return true if this object contains the given Object. - **/ - public boolean contains(Object object) - { - return vector.contains(object); + return (Object)get(size() - 1); } - - /** - * Performs the same function as Vector.removeElement() - **/ - public int indexOf(Object object) - { - if(!contains(object)) - return -1; - else - return vector.indexOf(object); - } - - /** - * Performs the same function as Vector.size() - */ - public int size() - { - return vector.size(); - } - - /** - * Performs the same function as Vector.removeAllElement() - **/ - public void removeAllElements() - { - vector.clear(); - } - - /** - * Performs the same function as Vector.removeElementAt() - **/ - public void removeElementAt(int index) - { - final Object object = (Object)vector.remove(index); - } - - /** - * Performs the same function as Vector.insertElementAt() - **/ - public final void insertElementAt(Object object, int index) - { - vector.add(index, object); - } - + /** * Insert an Object after another. * @param old_object The new_object will be inserted after this object @@ -155,9 +72,9 @@ public class FastVector final int old_object_index = indexOf(old_object); if(old_object_index == -1) - insertElementAt(new_object, 0); + add(0, new_object); else - insertElementAt(new_object, old_object_index + 1); + add(old_object_index + 1, new_object); } /** @@ -166,19 +83,8 @@ public class FastVector **/ public void setElementAt(final Object object, final int index) { - removeElementAt(index); - insertElementAt(object, index); - } - - /** - * Create a new FastVector with the same contents as this one. Note that - * this does only a shallow copy. - **/ - public Object clone() - { - final FastVector return_vector = new FastVector(); - return_vector.vector = (ArrayList)vector.clone(); - return return_vector; + remove(index); + add(index, object); } /** @@ -188,7 +94,7 @@ public class FastVector public FastVector sort(final Comparator cmp) { final FastVector return_vector = (FastVector)clone(); - Collections.sort(return_vector.vector, cmp); + Collections.sort(return_vector, cmp); return return_vector; }