+ /** */
+ @Override
+ public SequenceI findName(String name)
+ {
+ return findName(name, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ */
+ @Override
+ public SequenceI findName(String token, boolean b)
+ {
+ return findName(null, token, b);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
+ */
+ @Override
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
+
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
+ {
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i++) == startAfter)
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
+ }
+ while (i < sequences.size())
+ {
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
+ {
+ return getSequenceAt(i);
+ }
+
+ i++;
+ }
+
+ return null;
+ }
+
+ @Override
+ public SequenceI[] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
+ }
+
+ SequenceI[] result = new SequenceI[matches.size()];
+ for (i = 0; i < result.length; i++)
+ {
+ result[i] = (SequenceI) matches.elementAt(i);
+ }
+
+ return result;
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
+
+ i++;
+ }
+
+ return -1;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ @Override
+ public int findIndex(SearchResultsI results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return sequences.size();
+ }
+
+ @Override
+ public int getAbsoluteHeight()
+ {
+ return sequences.size() + getHiddenSequences().getSize();
+ }
+
+ @Override
+ public int getWidth()
+ {
+ int maxLength = -1;
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (getSequenceAt(i).getLength() > maxLength)
+ {
+ maxLength = getSequenceAt(i).getLength();
+ }
+ }
+
+ return maxLength;
+ }
+ /*
+ @Override
+ public int getWidth()
+ {
+ final Wrapper temp = new Wrapper();
+
+ forEachSequence(new Consumer<SequenceI>()
+ {
+ @Override
+ public void accept(SequenceI s)
+ {
+ if (s.getLength() > temp.inner)
+ {
+ temp.inner = s.getLength();
+ }
+ }
+ }, 0, sequences.size() - 1);
+
+ return temp.inner;
+ }
+
+ public static class Wrapper
+ {
+ public int inner;
+ }*/
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setGapCharacter(char gc)
+ {
+ gapCharacter = gc;
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
+ */
+ @Override
+ public boolean isAligned()
+ {
+ return isAligned(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ @Override
+ public boolean isAligned(boolean includeHidden)
+ {
+ int width = getWidth();
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
+ includeHidden = true; // no hidden sequences to check against.
+ }
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
+ {
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
+ }
+ }
+ }
+
+ return true;
+ }
+
+ @Override
+ public boolean isHidden(int alignmentIndex)
+ {
+ return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+ }
+
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ @Override
+ public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+ {
+ boolean result = false;
+ for (AlignmentAnnotation alan : getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated || includingAutoCalculated)
+ {
+ deleteAnnotation(alan);
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ @Override
+ public boolean deleteAnnotation(AlignmentAnnotation aa)
+ {
+ return deleteAnnotation(aa, true);
+ }
+
+ @Override
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
+ int aSize = 1;
+
+ if (annotations != null)
+ {
+ aSize = annotations.length;
+ }
+
+ if (aSize < 1)
+ {
+ return false;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+ boolean swap = false;
+ int tIndex = 0;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if (annotations[i] == aa)
+ {
+ swap = true;
+ continue;
+ }
+ if (tIndex < temp.length)
+ {
+ temp[tIndex++] = annotations[i];
+ }
+ }
+
+ if (swap)
+ {
+ annotations = temp;
+ if (unhook)
+ {
+ unhookAnnotation(aa);
+ }
+ }
+ return swap;
+ }
+
+ /**
+ * remove any object references associated with this annotation
+ *
+ * @param aa
+ */
+ private void unhookAnnotation(AlignmentAnnotation aa)
+ {
+ if (aa.sequenceRef != null)
+ {
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+ }
+ if (aa.groupRef != null)
+ {
+ // probably need to do more here in the future (post 2.5.0)
+ aa.groupRef = null;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ @Override
+ public void addAnnotation(AlignmentAnnotation aa)
+ {
+ addAnnotation(aa, -1);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation, int)
+ */
+ @Override
+ public void addAnnotation(AlignmentAnnotation aa, int pos)
+ {
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
+ }
+
+ int aSize = 1;
+ if (annotations != null)