// jalview.bin.Console.outPrintln(elapsed);
}
-
public static final ProfilesI calculateSS(List<SequenceI> list, int start,
int end, String source)
{
return calculateSS(list, start, end, false, source);
}
-
+
public static final ProfilesI calculateSS(List<SequenceI> sequences,
int start, int end, boolean profile, String source)
{
{
end = width;
}
-
- ProfilesI reply = calculateSS(seqs, width, start, end, profile, source);
+ ProfilesI reply = calculateSS(seqs, width, start, end, profile,
+ source);
return reply;
}
}
-
+
public static final ProfilesI calculateSS(final SequenceI[] sequences,
- int width, int start, int end, boolean saveFullProfile, String source)
+ int width, int start, int end, boolean saveFullProfile,
+ String source)
{
int seqCount = sequences.length;
-
+
int seqWithSSCount = 0;
-
+
ProfileI[] result = new ProfileI[width];
for (int column = start; column < end; column++)
{
-
+
int ssCount = 0;
-
+
SecondaryStructureCount ssCounts = new SecondaryStructureCount();
for (int row = 0; row < seqCount; row++)
"WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
-
+
char c = sequences[row].getCharAt(column);
- List<AlignmentAnnotation> annots = AlignmentUtils.getAlignmentAnnotationForSource(sequences[row], source);
- if(annots!=null) {
+ List<AlignmentAnnotation> annots = AlignmentUtils
+ .getAlignmentAnnotationForSource(sequences[row], source);
+ if (annots != null)
+ {
seqWithSSCount++;
- for(AlignmentAnnotation aa:annots) {
- if(aa!=null) {
+ for (AlignmentAnnotation aa : annots)
+ {
+ if (aa != null)
+ {
ssCount++;
}
-
- if (sequences[row].getLength() > column && !Comparison.isGap(c) && aa !=null)
+
+ if (sequences[row].getLength() > column && !Comparison.isGap(c)
+ && aa != null)
{
-
+
int seqPosition = sequences[row].findPosition(column);
-
- char ss = AlignmentUtils.findSSAnnotationForGivenSeqposition(
- aa, seqPosition);
- if(ss == '*') {
+
+ char ss = AlignmentUtils
+ .findSSAnnotationForGivenSeqposition(aa, seqPosition);
+ if (ss == '*')
+ {
continue;
- }
- ssCounts.add(ss);
+ }
+ ssCounts.add(ss);
}
- else if(Comparison.isGap(c) && aa!=null) {
+ else if (Comparison.isGap(c) && aa != null)
+ {
ssCounts.addGap();
}
}
int maxSSCount = ssCounts.getModalCount();
String maxSS = ssCounts.getSSForCount(maxSSCount);
int gapCount = ssCounts.getGapCount();
- ProfileI profile = new Profile(maxSS, ssCount, gapCount,
- maxSSCount, seqWithSSCount);
-
+ ProfileI profile = new Profile(maxSS, ssCount, gapCount, maxSSCount,
+ seqWithSSCount);
if (saveFullProfile)
{
// long elapsed = System.currentTimeMillis() - now;
// jalview.bin.Console.outPrintln(-elapsed);
}
-
-
- public static void completeSSConsensus(AlignmentAnnotation ssConsensus,
- ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
- boolean showSequenceLogo, long nseq)
- {
- // long now = System.currentTimeMillis();
- if (ssConsensus == null || ssConsensus.annotations == null
- || ssConsensus.annotations.length < endCol)
- {
- /*
+
+ public static void completeSSConsensus(AlignmentAnnotation ssConsensus,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
+ boolean showSequenceLogo, long nseq)
+ {
+ // long now = System.currentTimeMillis();
+ if (ssConsensus == null || ssConsensus.annotations == null
+ || ssConsensus.annotations.length < endCol)
+ {
+ /*
* called with a bad alignment annotation row
* wait for it to be initialised properly
*/
- return;
- }
-
- for (int i = startCol; i < endCol; i++)
- {
- ProfileI profile = profiles.get(i);
- if (profile == null)
- {
- /*
+ return;
+ }
+
+ for (int i = startCol; i < endCol; i++)
+ {
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
+ {
+ /*
* happens if sequences calculated over were
* shorter than alignment width
*/
- ssConsensus.annotations[i] = null;
- return;
- }
-
- if(ssConsensus.getNoOfSequencesIncluded()<0) {
- ssConsensus.setNoOfSequencesIncluded(profile.getSeqWithSSCount());
- }
-
- final int dp = getPercentageDp(nseq);
-
- float value = profile.getSSPercentageIdentity(ignoreGaps);
-
- String description = getSSTooltip(profile, value, showSequenceLogo,
- ignoreGaps, dp);
-
- String modalSS = profile.getModalSS();
- if ("".equals(modalSS))
- {
- modalSS = "-";
- }
- else if (modalSS.length() > 1)
- {
- modalSS = "+";
- }
- ssConsensus.annotations[i] = new Annotation(modalSS, description,
- ' ', value);
- }
-
- //Hide consensus with no data to display
- if(ssConsensus.getNoOfSequencesIncluded()<1)
- ssConsensus.visible = false;
-
- // long elapsed = System.currentTimeMillis() - now;
- // jalview.bin.Console.outPrintln(-elapsed);
- }
+ ssConsensus.annotations[i] = null;
+ return;
+ }
+
+ if (ssConsensus.getNoOfSequencesIncluded() < 0)
+ {
+ ssConsensus.setNoOfSequencesIncluded(profile.getSeqWithSSCount());
+ }
+
+ final int dp = getPercentageDp(nseq);
+
+ float value = profile.getSSPercentageIdentity(ignoreGaps);
+
+ String description = getSSTooltip(profile, value, showSequenceLogo,
+ ignoreGaps, dp);
+
+ String modalSS = profile.getModalSS();
+ if ("".equals(modalSS))
+ {
+ modalSS = "-";
+ }
+ else if (modalSS.length() > 1)
+ {
+ modalSS = "+";
+ }
+ ssConsensus.annotations[i] = new Annotation(modalSS, description, ' ',
+ value);
+ }
+
+ // Hide consensus with no data to display
+ if (ssConsensus.getNoOfSequencesIncluded() < 1)
+ ssConsensus.visible = false;
+
+ // long elapsed = System.currentTimeMillis() - now;
+ // jalview.bin.Console.outPrintln(-elapsed);
+ }
/**
* Derive the gap count annotation row.
}
return description;
}
-
+
static String getSSTooltip(ProfileI profile, float pid,
boolean showSequenceLogo, boolean ignoreGaps, int dp)
{
{
char[] symbols;
int[] values;
-
+
if (profile.getCounts() != null)
{
ResidueCount counts = profile.getCounts();
SymbolCounts symbolCounts = counts.getSymbolCounts();
symbols = symbolCounts.symbols;
values = symbolCounts.values;
-
+
}
- else if(profile.getSSCounts() != null)
+ else if (profile.getSSCounts() != null)
{
SecondaryStructureCount counts = profile.getSSCounts();
// to do
- SecondaryStructureCount.SymbolCounts symbolCounts = counts.getSymbolCounts();
+ SecondaryStructureCount.SymbolCounts symbolCounts = counts
+ .getSymbolCounts();
symbols = symbolCounts.symbols;
values = symbolCounts.values;
}
- else {
+ else
+ {
return null;
}
-
QuickSort.sort(values, symbols);
int totalPercentage = 0;
private static final int DEFAULT_OPENCOST = 120;
private static final int DEFAULT_EXTENDCOST = 20;
-
- private int GAP_OPEN_COST=DEFAULT_OPENCOST;
- private int GAP_EXTEND_COST=DEFAULT_EXTENDCOST;
+ private int GAP_OPEN_COST = DEFAULT_OPENCOST;
+
+ private int GAP_EXTEND_COST = DEFAULT_EXTENDCOST;
private static final int GAP_INDEX = -1;
int[] aseq1;
int[] aseq2;
-
+
/*
* matches in alignment
*/
- int match=-1;
+ int match = -1;
public String astr1 = "";
public float maxscore;
- public float meanScore; //needed for PaSiMap
+ public float meanScore; // needed for PaSiMap
- public int hypotheticMaxScore; // needed for PaSiMap
+ public int hypotheticMaxScore; // needed for PaSiMap
int prev = 0;
GAP_OPEN_COST = opencost;
GAP_EXTEND_COST = extcost;
}
+
public AlignSeq(SequenceI s1, SequenceI s2, String type)
{
seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
public AlignSeq(SequenceI s1, SequenceI s2, String type, int opencost,
int extcost)
{
- this(s1,s2,type);
- GAP_OPEN_COST=opencost;
- GAP_EXTEND_COST=extcost;
+ this(s1, s2, type);
+ GAP_OPEN_COST = opencost;
+ GAP_EXTEND_COST = extcost;
}
public AlignSeq(SequenceI s12, String string1, SequenceI s22,
String string2, String type2, int defaultOpencost,
int defaultExtendcost)
{
- this(s12,string1,s22,string2,type2);
- GAP_OPEN_COST=defaultOpencost;
- GAP_EXTEND_COST=defaultExtendcost;
+ this(s12, string1, s22, string2, type2);
+ GAP_OPEN_COST = defaultOpencost;
+ GAP_EXTEND_COST = defaultExtendcost;
}
/**
}
/**
- * returns the overall score of the alignment
- *
- * @return
- */
+ * returns the overall score of the alignment
+ *
+ * @return
+ */
public float getAlignmentScore()
{
return alignmentScore;
s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
return alSeq2;
}
+
/**
* fraction of seq2 matched in the alignment
+ *
* @return NaN or [0..1]
*/
public double getS2Coverage()
{
- if (match>=0)
+ if (match >= 0)
{
- return ((double)match)/((double)s2.getEnd()-s2.getStart()+1);
+ return ((double) match) / ((double) s2.getEnd() - s2.getStart() + 1);
}
return Double.NaN;
}
+
/**
* fraction of seq1 matched in the alignment
+ *
* @return NaN or [0..1]
*/
public double getS1Coverage()
{
- if (match>=0)
+ if (match >= 0)
{
- return ((double)match)/((double)s1.getEnd()-s1.getStart()+1);
+ return ((double) match) / ((double) s1.getEnd() - s1.getStart() + 1);
}
return Double.NaN;
}
public void seqInit(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1,string1,s2,string2,type,GAP_OPEN_COST,GAP_EXTEND_COST);
+ seqInit(s1, string1, s2, string2, type, GAP_OPEN_COST, GAP_EXTEND_COST);
}
+
public void seqInit(SequenceI s1, String string1, SequenceI s2,
- String string2, String type, int opening,int extension)
+ String string2, String type, int opening, int extension)
{
- GAP_OPEN_COST=opening;
- GAP_EXTEND_COST=extension;
+ GAP_OPEN_COST = opening;
+ GAP_EXTEND_COST = extension;
this.s1 = s1;
this.s2 = s2;
setDefaultParams(type);
aseq1 = new int[seq1.length + seq2.length];
aseq2 = new int[seq1.length + seq2.length];
- match=0;
+ match = 0;
StringBuilder sb1 = new StringBuilder(aseq1.length);
StringBuilder sb2 = new StringBuilder(aseq2.length);
count = (seq1.length + seq2.length) - 1;
-
while (i > 0 && j > 0)
{
aseq1[count] = seq1[i];
{
aseq2[count] = seq2[j];
sb2.append(s2str.charAt(j));
- if (aseq1[count]!=GAP_INDEX) {
+ if (aseq1[count] != GAP_INDEX)
+ {
match++;
}
}
-
/*
* we built the character strings backwards, so now
* reverse them to convert to sequence strings
int trace;
maxscore = score[i][j] / 10f;
- //prepare trailing gaps
+ // prepare trailing gaps
while ((i < seq1.length - 1) || (j < seq2.length - 1))
{
i++;
count = (seq1.length + seq2.length) - 1;
- //get trailing gaps
+ // get trailing gaps
while ((i >= seq1.length) || (j >= seq2.length))
{
if (i >= seq1.length)
{
- aseq1[count] = GAP_INDEX;
- sb1.append("-");
- aseq2[count] = seq2[j];
- sb2.append(s2str.charAt(j));
- } else if (j >= seq2.length) {
- aseq1[count] = seq1[i];
- sb1.append(s1str.charAt(i));
- aseq2[count] = GAP_INDEX;
- sb2.append("-");
+ aseq1[count] = GAP_INDEX;
+ sb1.append("-");
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+ }
+ else if (j >= seq2.length)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = GAP_INDEX;
+ sb2.append("-");
}
i--;
j--;
aseq2[count] = seq2[j];
sb2.append(s2str.charAt(j));
- //get initial gaps
+ // get initial gaps
while (j > 0 || i > 0)
{
if (j > 0)
{
- j--;
- sb1.append("-");
- sb2.append(s2str.charAt(j));
- } else if (i > 0) {
- i--;
- sb1.append(s1str.charAt(i));
- sb2.append("-");
+ j--;
+ sb1.append("-");
+ sb2.append(s2str.charAt(j));
+ }
+ else if (i > 0)
+ {
+ i--;
+ sb1.append(s1str.charAt(i));
+ sb2.append("-");
}
}
{
int n = seq1.length;
int m = seq2.length;
- final int GAP_EX_COST=GAP_EXTEND_COST;
+ final int GAP_EX_COST = GAP_EXTEND_COST;
final int GAP_OP_COST = GAP_OPEN_COST;
// top left hand element
score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(j));
- score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST,
- -GAP_EX_COST);
+ score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST, -GAP_EX_COST);
traceback[0][j] = 1;
}
public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
String type)
{
- return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,DEFAULT_EXTENDCOST);
+ return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,
+ DEFAULT_EXTENDCOST);
}
+
public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
- String type, int opencost,int extcost)
+ String type, int opencost, int extcost)
{
-
- AlignSeq as = new AlignSeq(s1, s2, type,opencost,extcost);
+
+ AlignSeq as = new AlignSeq(s1, s2, type, opencost, extcost);
as.calcScoreMatrix();
as.traceAlignment();
}
/**
- * calculate the mean score of the alignment
- * mean score is equal to the score of an alignmenet of two sequences with randomly shuffled AA sequence composited of the same AA as the two original sequences
- *
- */
+ * calculate the mean score of the alignment mean score is equal to the score
+ * of an alignmenet of two sequences with randomly shuffled AA sequence
+ * composited of the same AA as the two original sequences
+ *
+ */
public void meanScore()
{
- int length = indelfreeAstr1.length(); //both have the same length
- //create HashMap for counting residues in each sequence
+ int length = indelfreeAstr1.length(); // both have the same length
+ // create HashMap for counting residues in each sequence
HashMap<Character, Integer> seq1ResCount = new HashMap<Character, Integer>();
HashMap<Character, Integer> seq2ResCount = new HashMap<Character, Integer>();
- // for both sequences (String indelfreeAstr1 or 2) create a key for the residue and add 1 each time its encountered
- for (char residue: indelfreeAstr1.toCharArray())
+ // for both sequences (String indelfreeAstr1 or 2) create a key for the
+ // residue and add 1 each time its encountered
+ for (char residue : indelfreeAstr1.toCharArray())
{
seq1ResCount.putIfAbsent(residue, 0);
seq1ResCount.replace(residue, seq1ResCount.get(residue) + 1);
}
- for (char residue: indelfreeAstr2.toCharArray())
+ for (char residue : indelfreeAstr2.toCharArray())
{
seq2ResCount.putIfAbsent(residue, 0);
seq2ResCount.replace(residue, seq2ResCount.get(residue) + 1);
}
- // meanscore = for each residue pair get the number of appearance and add (countA * countB * pairwiseScore(AB))
+ // meanscore = for each residue pair get the number of appearance and add
+ // (countA * countB * pairwiseScore(AB))
// divide the meanscore by the sequence length afterwards
float _meanscore = 0;
for (char resA : seq1ResCount.keySet())
{
for (char resB : seq2ResCount.keySet())
{
- int countA = seq1ResCount.get(resA);
- int countB = seq2ResCount.get(resB);
+ int countA = seq1ResCount.get(resA);
+ int countB = seq2ResCount.get(resB);
float scoreAB = scoreMatrix.getPairwiseScore(resA, resB);
- _meanscore += countA * countB * scoreAB;
+ _meanscore += countA * countB * scoreAB;
}
}
_meanscore /= length;
}
/**
- * calculate the hypothetic max score using the self-alignment of the sequences
- */
+ * calculate the hypothetic max score using the self-alignment of the
+ * sequences
+ */
public void hypotheticMaxScore()
{
int _hmsA = 0;
int _hmsB = 0;
- for (char residue: indelfreeAstr1.toCharArray())
+ for (char residue : indelfreeAstr1.toCharArray())
{
_hmsA += scoreMatrix.getPairwiseScore(residue, residue);
}
- for (char residue: indelfreeAstr2.toCharArray())
+ for (char residue : indelfreeAstr2.toCharArray())
{
_hmsB += scoreMatrix.getPairwiseScore(residue, residue);
}
- this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower self alignment
+ this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower
+ // self alignment
}
}
/**
- * create strings based of astr1 and astr2 but without gaps
- */
+ * create strings based of astr1 and astr2 but without gaps
+ */
public void getIndelfreeAstr()
{
- int n = astr1.length(); // both have the same length
+ int n = astr1.length(); // both have the same length
for (int i = 0; i < n; i++)
{
- if (Character.isLetter(astr1.charAt(i)) && Character.isLetter(astr2.charAt(i))) // if both sequences dont have a gap -> add to indelfreeAstr
+ if (Character.isLetter(astr1.charAt(i))
+ && Character.isLetter(astr2.charAt(i))) // if both sequences dont
+ // have a gap -> add to
+ // indelfreeAstr
{
- this.indelfreeAstr1 += astr1.charAt(i);
- this.indelfreeAstr2 += astr2.charAt(i);
+ this.indelfreeAstr1 += astr1.charAt(i);
+ this.indelfreeAstr2 += astr2.charAt(i);
}
}
}
/**
- * calculates the overall score of the alignment
- * preprescore = sum of all scores - all penalties
- * if preprescore < 1 ~ alignmentScore = Float.NaN >
- * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore - meanScore)) * coverage
- */
+ * calculates the overall score of the alignment preprescore = sum of all
+ * scores - all penalties if preprescore < 1 ~ alignmentScore = Float.NaN >
+ * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore -
+ * meanScore)) * coverage
+ */
public void scoreAlignment()
{
char char2 = indelfreeAstr2.charAt(i);
boolean aIsLetter = Character.isLetter(char1);
boolean bIsLetter = Character.isLetter(char2);
- if (aIsLetter && bIsLetter) // if pair -> get score
+ if (aIsLetter && bIsLetter) // if pair -> get score
{
score += scoreMatrix.getPairwiseScore(char1, char2);
- } else if (!aIsLetter && !bIsLetter) { // both are gap -> skip
- } else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen)) { // one side gapopen -> score - gap_extend
- score -= GAP_EXTEND_COST;
- } else { // no gap open -> score - gap_open
- score -= GAP_OPEN_COST;
+ }
+ else if (!aIsLetter && !bIsLetter)
+ { // both are gap -> skip
+ }
+ else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen))
+ { // one side gapopen -> score - gap_extend
+ score -= GAP_EXTEND_COST;
+ }
+ else
+ { // no gap open -> score - gap_open
+ score -= GAP_OPEN_COST;
}
// adjust GapOpen status in both sequences
aGapOpen = (!aIsLetter) ? true : false;
bGapOpen = (!bIsLetter) ? true : false;
}
- float preprescore = score; // if this score < 1 --> alignment score = Float.NaN
- score = (score - this.meanScore) / (this.hypotheticMaxScore - this.meanScore);
- int[] _max = MiscMath.findMax(new int[]{astr1.replace("-","").length(), astr2.replace("-","").length()}); // {index of max, max}
- float coverage = (float) n / (float) _max[1]; // indelfreeAstr length / longest sequence length
- float prescore = score; // only debug
+ float preprescore = score; // if this score < 1 --> alignment score =
+ // Float.NaN
+ score = (score - this.meanScore)
+ / (this.hypotheticMaxScore - this.meanScore);
+ int[] _max = MiscMath
+ .findMax(new int[]
+ { astr1.replace("-", "").length(),
+ astr2.replace("-", "").length() }); // {index of max, max}
+ float coverage = (float) n / (float) _max[1]; // indelfreeAstr length /
+ // longest sequence length
+ float prescore = score; // only debug
score *= coverage;
- //System.out.println(String.format("prepre-score: %f, pre-score: %f, longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, _max[1], score, this.meanScore, this.hypotheticMaxScore));
+ // System.out.println(String.format("prepre-score: %f, pre-score: %f,
+ // longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore,
+ // _max[1], score, this.meanScore, this.hypotheticMaxScore));
float minScore = 0f;
this.alignmentScore = (score <= minScore) ? Float.NaN : score;
}
public void setScoreMatrix(ScoreMatrix sm)
{
- if (sm != null) {
- scoreMatrix = sm;
- }
+ if (sm != null)
+ {
+ scoreMatrix = sm;
+ }
}
}
});
}
}
-
-
+
/**
* Returns a BitSet (possibly empty) of those graphGroups for line graph
* annotations, which have at least one member annotation row marked visible.
{
private static final int CODON_LENGTH = 3;
- private static final String SEQUENCE_VARIANT = "sequence_variant:";
+ private static final String SEQUENCE_VARIANT = "sequence_variant:";
/*
* the 'id' attribute is provided for variant features fetched from
}
}
}
-
-
- public static boolean isSSAnnotationPresent( Map<SequenceI, List<AlignmentAnnotation>> annotations) {
-
+
+ public static boolean isSSAnnotationPresent(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations)
+ {
+
for (SequenceI seq : annotations.keySet())
{
- if(isSecondaryStructurePresent(annotations.get(seq).toArray(new AlignmentAnnotation[0])))
+ if (isSecondaryStructurePresent(
+ annotations.get(seq).toArray(new AlignmentAnnotation[0])))
{
return true;
}
}
}
}
-
+
/**
* Shows or hides auto calculated annotations for a sequence group.
*
}
}
}
-
-
+
public static AlignmentAnnotation getFirstSequenceAnnotationOfType(
AlignmentI al, int graphType)
{
}
return true;
}
-
- public static boolean isSecondaryStructurePresent(AlignmentAnnotation[] annotations)
+
+ public static boolean isSecondaryStructurePresent(
+ AlignmentAnnotation[] annotations)
{
boolean ssPresent = false;
return ssPresent;
}
-
+
public static Color getSecondaryStructureAnnotationColour(char symbol)
{
return Color.white;
}
- public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation aa,
- int seqPosition)
+ public static char findSSAnnotationForGivenSeqposition(
+ AlignmentAnnotation aa, int seqPosition)
{
char ss = '*';
return ss;
}
-
-
+
public static List<String> extractSSSourceInAlignmentAnnotation(
AlignmentAnnotation[] annotations)
{
return ssSources;
}
-
+
public static String extractSSSourceFromAnnotationDescription(
AlignmentAnnotation aa)
{
if (label.equals(aa.label))
{
- if (aa.getProperty(Constants.SS_PROVIDER_PROPERTY) != null)
+ if (aa.getProperty(Constants.SS_PROVIDER_PROPERTY) != null)
{
-
+
return aa.getProperty(Constants.SS_PROVIDER_PROPERTY);
-
+
}
-
+
// For JPred
if (Constants.SS_ANNOTATION_FROM_JPRED_LABEL.equals(aa.label))
{
// For input with secondary structure
if (Constants.SS_ANNOTATION_LABEL.equals(aa.label)
- && aa.description != null && Constants.SS_ANNOTATION_LABEL.equals(aa.description))
+ && aa.description != null
+ && Constants.SS_ANNOTATION_LABEL.equals(aa.description))
{
return (Constants.SECONDARY_STRUCTURE_LABELS.get(aa.label));
String entryProvider = entry.getProvider();
if (entryProvider == null)
{
- // No provider - so this is either an old Jalview project, or not retrieved from recognised source
+ // No provider - so this is either an old Jalview project, or not
+ // retrieved from recognised source
entryProvider = "PDB";
}
- // Should (re)use a standard mechanism for extracting the PDB ID as it is written 1QWXTUV:CHAIN
+ // Should (re)use a standard mechanism for extracting the PDB ID as it
+ // is written 1QWXTUV:CHAIN
// Trim the string from first occurrence of colon
String entryID = entry.getId();
int index = entryID.indexOf(':');
}
- // TODO: shouldn't need to extract from description what the originating ID is for this annotation!
+ // TODO: shouldn't need to extract from description what the
+ // originating ID is for this annotation!
if (entryProvider == "PDB" && aa.description.toLowerCase()
.contains("secondary structure for "
+ entryID.toLowerCase()))
return null;
}
-
- //to do set priority for labels
+
+ // to do set priority for labels
public static List<AlignmentAnnotation> getAlignmentAnnotationForSource(
SequenceI seq, String ssSource)
{
for (AlignmentAnnotation annot : aa)
{
- String ssSourceForAnnot = extractSSSourceFromAnnotationDescription(annot);
- if (ssSourceForAnnot != null && ssSource
- .equals(ssSourceForAnnot))
+ String ssSourceForAnnot = extractSSSourceFromAnnotationDescription(
+ annot);
+ if (ssSourceForAnnot != null && ssSource.equals(ssSourceForAnnot))
{
ssAnnots.add(annot);
}
*
* @param selectedSSSource
* @param aa
- * @return true if aa is from a provider or all providers as specified by selectedSSSource
+ * @return true if aa is from a provider or all providers as specified by
+ * selectedSSSource
*/
public static boolean isSecondaryStructureFrom(String selectedSSSource,
AlignmentAnnotation aa)
public class ConnectivityException extends RuntimeException
{
private String sequence;
+
private int connection;
+
private byte dim;
public ConnectivityException(String sequence, int connection, byte dim)
this("Insufficient number of connections", sequence, connection, dim);
}
- public ConnectivityException(String message, String sequence, int connection, byte dim)
+ public ConnectivityException(String message, String sequence,
+ int connection, byte dim)
{
- super(String.format("%s for %s (%d, should be %d or more)", message, sequence, connection, dim));
+ super(String.format("%s for %s (%d, should be %d or more)", message,
+ sequence, connection, dim));
this.sequence = sequence;
this.connection = connection;
this.dim = dim;
}
else
{
- //allFeatures = sf.getAllFeatures(null);
+ // allFeatures = sf.getAllFeatures(null);
allFeatures = sf.getAllFeatures();
}
// so we can check we are advancing when debugging
/**
* Performs Principal Component Analysis on given sequences
- * @AUTHOR MorellThomas
+ *
+ * @AUTHOR MorellThomas
*/
public class PaSiMap implements Runnable
{
* @param sm
* @param options
*/
- public PaSiMap(AlignmentViewport sequences, ScoreModelI sm, PairwiseAlignPanel pap)
+ public PaSiMap(AlignmentViewport sequences, ScoreModelI sm,
+ PairwiseAlignPanel pap)
{
this.seqs = sequences;
- if (sm!=null && sm instanceof ScoreMatrix)
+ if (sm != null && sm instanceof ScoreMatrix)
{
this.scoreMatrix = ((ScoreMatrix) sm);
- } else {
+ }
+ else
+ {
this.scoreMatrix = null;
}
* DOCUMENT ME!
* @param mm
* DOCUMENT ME!
- * @param factor ~ is 1
+ * @param factor
+ * ~ is 1
*
* @return DOCUMENT ME!
*/
}
/**
- * Answers a formatted text report of the PaSiMap calculation results (matrices
- * and eigenvalues) suitable for display
+ * Answers a formatted text report of the PaSiMap calculation results
+ * (matrices and eigenvalues) suitable for display
*
* @return
*/
/**
* Performs the PaSiMap calculation
*
- * creates a new gui/PairwiseAlignPanel with the input sequences (AlignmentViewport)
- * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the AlignmentScores (float for each pair)
- * gets all float[][] scores from the gui/PairwiseAlignPanel
- * checks the connections for each sequence with AlignmentViewport seqs.calculateConnectivity(float[][] scores, int dim) (from analysis/Connectivity) -- throws an Exception if insufficient
- * creates a math/MatrixI pairwiseScores of the float[][] scores
- * copys the scores and fills the diagonal to create a symmetric matrix using math/Matrix.fillDiagonal()
- * performs the analysis/ccAnalysis with the symmetric matrix
- * gets the eigenmatrix and the eigenvalues using math/Matrix.tqli()
+ * creates a new gui/PairwiseAlignPanel with the input sequences
+ * (AlignmentViewport) uses analysis/AlignSeq to creatue the pairwise
+ * alignments and calculate the AlignmentScores (float for each pair) gets all
+ * float[][] scores from the gui/PairwiseAlignPanel checks the connections for
+ * each sequence with AlignmentViewport seqs.calculateConnectivity(float[][]
+ * scores, int dim) (from analysis/Connectivity) -- throws an Exception if
+ * insufficient creates a math/MatrixI pairwiseScores of the float[][] scores
+ * copys the scores and fills the diagonal to create a symmetric matrix using
+ * math/Matrix.fillDiagonal() performs the analysis/ccAnalysis with the
+ * symmetric matrix gets the eigenmatrix and the eigenvalues using
+ * math/Matrix.tqli()
*/
@Override
public void run()
{
try
{
- //alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
+ // alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
alignment.calculate(scoreMatrix);
- float[][] scores = alignment.getAlignmentScores(); //bigger index first -- eg scores[14][13]
+ float[][] scores = alignment.getAlignmentScores(); // bigger index first
+ // -- eg scores[14][13]
SequenceI[] iseqs = alignment.getInputSequences();
Connectivity.getConnectivity(iseqs, scores, dim);
public static final String NEIGHBOUR_JOINING = "NJ";
protected SequenceI[] sequences;
+
protected List<String> labels;
public AlignmentView seqData;
}
init(seqStrings, start, end);
-
+
computeTree(sm, scoreParameters);
}
return sequences;
}
-
/**
*
* @return true if tree has real distances
labels = new ArrayList<String>();
sequences = sm.expandSeqData(sequences, seqData, scoreOptions, labels);
noseqs = sequences.length;
-
+
distances = sm.findDistances(seqData, scoreOptions);
makeLeaves();
SequenceNode sn = new SequenceNode();
sn.setElement(sequences[i]);
-
- if (labels.size()==noseqs)
+
+ if (labels.size() == noseqs)
{
sn.setLabel(labels.get(i));
}
-
+
sn.setName(sequences[i].getName());
-
+
node.addElement(sn);
BitSet bs = new BitSet();
bs.set(i);
if (leafAnnotations != null)
{
// leaf names are seuqence ID + annotation for display
- // leaf links are annotationId <> annotation object for import from project
+ // leaf links are annotationId <> annotation object for import from
+ // project
// --> need to resolve before passing for display
// ==> do leafs need to be renamed after import ?
- // ==> implies the 'nodeLabel' business needs to be callable independently of score function
- } else {
+ // ==> implies the 'nodeLabel' business needs to be callable independently
+ // of score function
+ }
+ else
+ {
associateLeavesToSequences(seqs);
}
}
/**
* A class to model rectangular matrices of double values and operations on them
*/
-public class ccAnalysis
+public class ccAnalysis
{
- private byte dim = 0; //dimensions
+ private byte dim = 0; // dimensions
- private MatrixI scoresOld; //input scores
+ private MatrixI scoresOld; // input scores
public ccAnalysis(MatrixI scores, byte dim)
{
{
for (int j = 0; j < scores.width(); j++)
{
- if (!Double.isNaN(scores.getValue(i,j)))
- {
- scores.setValue(i, j, (double) Math.round(scores.getValue(i,j) * (int) 10000) / 10000);
- }
+ if (!Double.isNaN(scores.getValue(i, j)))
+ {
+ scores.setValue(i, j,
+ (double) Math.round(scores.getValue(i, j) * (int) 10000)
+ / 10000);
+ }
}
}
this.scoresOld = scores;
this.dim = dim;
}
- /**
- * Initialise a distrust-score for each hypothesis (h) of hSigns
- * distrust = conHypNum - proHypNum
- *
- * @param hSigns ~ hypothesis signs (+/-) for each sequence
- * @param scores ~ input score matrix
- *
- * @return distrustScores
- */
+ /**
+ * Initialise a distrust-score for each hypothesis (h) of hSigns distrust =
+ * conHypNum - proHypNum
+ *
+ * @param hSigns
+ * ~ hypothesis signs (+/-) for each sequence
+ * @param scores
+ * ~ input score matrix
+ *
+ * @return distrustScores
+ */
private int[] initialiseDistrusts(byte[] hSigns, MatrixI scores)
{
int[] distrustScores = new int[scores.width()];
-
+
// loop over symmetric matrix
for (int i = 0; i < scores.width(); i++)
{
for (int j = 0; j < scores.width(); j++)
{
- double cell = scores.getRow(i)[j]; // value at [i][j] in scores
- byte hBSign = hSigns[j];
- if (!Double.isNaN(cell))
- {
- byte cellSign = (byte) Math.signum(cell); //check if sign of matrix value fits hyptohesis
- if (cellSign == hASign * hBSign)
- {
- proHypNum++;
- } else {
- conHypNum++;
- }
- }
+ double cell = scores.getRow(i)[j]; // value at [i][j] in scores
+ byte hBSign = hSigns[j];
+ if (!Double.isNaN(cell))
+ {
+ byte cellSign = (byte) Math.signum(cell); // check if sign of matrix
+ // value fits hyptohesis
+ if (cellSign == hASign * hBSign)
+ {
+ proHypNum++;
+ }
+ else
+ {
+ conHypNum++;
+ }
+ }
}
- distrustScores[i] = conHypNum - proHypNum; //create distrust score for each sequence
+ distrustScores[i] = conHypNum - proHypNum; // create distrust score for
+ // each sequence
}
return distrustScores;
}
/**
- * Optemise hypothesis concerning the sign of the hypothetical value for each hSigns by interpreting the pairwise correlation coefficients as scalar products
- *
- * @param hSigns ~ hypothesis signs (+/-)
- * @param distrustScores
- * @param scores ~ input score matrix
- *
- * @return hSigns
- */
- private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores, MatrixI scores)
+ * Optemise hypothesis concerning the sign of the hypothetical value for each
+ * hSigns by interpreting the pairwise correlation coefficients as scalar
+ * products
+ *
+ * @param hSigns
+ * ~ hypothesis signs (+/-)
+ * @param distrustScores
+ * @param scores
+ * ~ input score matrix
+ *
+ * @return hSigns
+ */
+ private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores,
+ MatrixI scores)
{
// get maximum distrust score
int[] maxes = MiscMath.findMax(distrustScores);
// if hypothesis is not optimal yet
if (maxDistrust > 0)
{
- //toggle sign for hI with maximum distrust
+ // toggle sign for hI with maximum distrust
hSigns[maxDistrustIndex] *= -1;
// update distrust at same position
distrustScores[maxDistrustIndex] *= -1;
byte hASign = hSigns[maxDistrustIndex];
for (int NOTmaxDistrustIndex = 0; NOTmaxDistrustIndex < distrustScores.length; NOTmaxDistrustIndex++)
{
- if (NOTmaxDistrustIndex != maxDistrustIndex)
- {
- byte hBSign = hSigns[NOTmaxDistrustIndex];
- double cell = scores.getValue(maxDistrustIndex, NOTmaxDistrustIndex);
-
- // distrust only changed if not NaN
- if (!Double.isNaN(cell))
- {
- byte cellSign = (byte) Math.signum(cell);
- // if sign of cell matches hypothesis decrease distrust by 2 because 1 more value supporting and 1 less contradicting
- // else increase by 2
- if (cellSign == hASign * hBSign)
- {
- distrustScores[NOTmaxDistrustIndex] -= 2;
- } else {
- distrustScores[NOTmaxDistrustIndex] += 2;
- }
- }
- }
+ if (NOTmaxDistrustIndex != maxDistrustIndex)
+ {
+ byte hBSign = hSigns[NOTmaxDistrustIndex];
+ double cell = scores.getValue(maxDistrustIndex,
+ NOTmaxDistrustIndex);
+
+ // distrust only changed if not NaN
+ if (!Double.isNaN(cell))
+ {
+ byte cellSign = (byte) Math.signum(cell);
+ // if sign of cell matches hypothesis decrease distrust by 2 because
+ // 1 more value supporting and 1 less contradicting
+ // else increase by 2
+ if (cellSign == hASign * hBSign)
+ {
+ distrustScores[NOTmaxDistrustIndex] -= 2;
+ }
+ else
+ {
+ distrustScores[NOTmaxDistrustIndex] += 2;
+ }
+ }
+ }
}
- //further optimisation necessary
+ // further optimisation necessary
return optimiseHypothesis(hSigns, distrustScores, scores);
- } else {
+ }
+ else
+ {
return hSigns;
}
}
- /**
- * takes the a symmetric MatrixI as input scores which may contain Double.NaN
- * approximate the missing values using hypothesis optimisation
- *
- * runs analysis
- *
- * @param scores ~ score matrix
- *
- * @return
- */
- public MatrixI run () throws Exception
+ /**
+ * takes the a symmetric MatrixI as input scores which may contain Double.NaN
+ * approximate the missing values using hypothesis optimisation
+ *
+ * runs analysis
+ *
+ * @param scores
+ * ~ score matrix
+ *
+ * @return
+ */
+ public MatrixI run() throws Exception
{
- //initialse eigenMatrix and repMatrix
+ // initialse eigenMatrix and repMatrix
MatrixI eigenMatrix = scoresOld.copy();
MatrixI repMatrix = scoresOld.copy();
try
{
- /*
- * Calculate correction factor for 2nd and higher eigenvalue(s).
- * This correction is NOT needed for the 1st eigenvalue, because the
- * unknown (=NaN) values of the matrix are approximated by presuming
- * 1-dimensional vectors as the basis of the matrix interpretation as dot
- * products.
- */
-
- System.out.println("Input correlation matrix:");
- eigenMatrix.print(System.out, "%1.4f ");
-
- int matrixWidth = eigenMatrix.width(); // square matrix, so width == height
- int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); //total number of elemts
-
- float correctionFactor = (float) (matrixElementsTotal - eigenMatrix.countNaN()) / (float) matrixElementsTotal;
-
- /*
- * Calculate hypothetical value (1-dimensional vector) h_i for each
- * dataset by interpreting the given correlation coefficients as scalar
- * products.
- */
-
- /*
- * Memory for current hypothesis concerning sign of each h_i.
- * List of signs for all h_i in the encoding:
+ /*
+ * Calculate correction factor for 2nd and higher eigenvalue(s).
+ * This correction is NOT needed for the 1st eigenvalue, because the
+ * unknown (=NaN) values of the matrix are approximated by presuming
+ * 1-dimensional vectors as the basis of the matrix interpretation as dot
+ * products.
+ */
+
+ System.out.println("Input correlation matrix:");
+ eigenMatrix.print(System.out, "%1.4f ");
+
+ int matrixWidth = eigenMatrix.width(); // square matrix, so width ==
+ // height
+ int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); // total number
+ // of elemts
+
+ float correctionFactor = (float) (matrixElementsTotal
+ - eigenMatrix.countNaN()) / (float) matrixElementsTotal;
+
+ /*
+ * Calculate hypothetical value (1-dimensional vector) h_i for each
+ * dataset by interpreting the given correlation coefficients as scalar
+ * products.
+ */
+
+ /*
+ * Memory for current hypothesis concerning sign of each h_i.
+ * List of signs for all h_i in the encoding:
* * 1: positive
* * 0: zero
* * -1: negative
- * Initial hypothesis: all signs are positive.
- */
- byte[] hSigns = new byte[matrixWidth];
- Arrays.fill(hSigns, (byte) 1);
-
- //Estimate signs for each h_i by refining hypothesis on signs.
- hSigns = optimiseHypothesis(hSigns, initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix);
-
-
- //Estimate absolute values for each h_i by determining sqrt of mean of
- //non-NaN absolute values for every row.
- double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow());
-
- //Combine estimated signs with absolute values in obtain total value for
- //each h_i.
- double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs);
-
- /*Complement symmetric matrix by using the scalar products of estimated
- *values of h_i to replace NaN-cells.
- *Matrix positions that have estimated values
- *(only for diagonal and upper off-diagonal values, due to the symmetry
- *the positions of the lower-diagonal values can be inferred).
- List of tuples (row_idx, column_idx).*/
-
- ArrayList<int[]> estimatedPositions = new ArrayList<int[]>();
-
- // for off-diagonal cells
- for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++)
- {
- for (int columnIndex = rowIndex + 1; columnIndex < matrixWidth; columnIndex++)
+ * Initial hypothesis: all signs are positive.
+ */
+ byte[] hSigns = new byte[matrixWidth];
+ Arrays.fill(hSigns, (byte) 1);
+
+ // Estimate signs for each h_i by refining hypothesis on signs.
+ hSigns = optimiseHypothesis(hSigns,
+ initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix);
+
+ // Estimate absolute values for each h_i by determining sqrt of mean of
+ // non-NaN absolute values for every row.
+ double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow());
+
+ // Combine estimated signs with absolute values in obtain total value for
+ // each h_i.
+ double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs);
+
+ /*Complement symmetric matrix by using the scalar products of estimated
+ *values of h_i to replace NaN-cells.
+ *Matrix positions that have estimated values
+ *(only for diagonal and upper off-diagonal values, due to the symmetry
+ *the positions of the lower-diagonal values can be inferred).
+ List of tuples (row_idx, column_idx).*/
+
+ ArrayList<int[]> estimatedPositions = new ArrayList<int[]>();
+
+ // for off-diagonal cells
+ for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++)
{
- double cell = eigenMatrix.getValue(rowIndex, columnIndex);
- if (Double.isNaN(cell))
- {
- //calculate scalar product as new cell value
- cell = hValues[rowIndex] * hValues[columnIndex];
- //fill in new value in cell and symmetric partner
- eigenMatrix.setValue(rowIndex, columnIndex, cell);
- eigenMatrix.setValue(columnIndex, rowIndex, cell);
- //save positions of estimated values
- estimatedPositions.add(new int[]{rowIndex, columnIndex});
- }
+ for (int columnIndex = rowIndex
+ + 1; columnIndex < matrixWidth; columnIndex++)
+ {
+ double cell = eigenMatrix.getValue(rowIndex, columnIndex);
+ if (Double.isNaN(cell))
+ {
+ // calculate scalar product as new cell value
+ cell = hValues[rowIndex] * hValues[columnIndex];
+ // fill in new value in cell and symmetric partner
+ eigenMatrix.setValue(rowIndex, columnIndex, cell);
+ eigenMatrix.setValue(columnIndex, rowIndex, cell);
+ // save positions of estimated values
+ estimatedPositions.add(new int[] { rowIndex, columnIndex });
+ }
+ }
}
- }
- // for diagonal cells
- for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++)
+ // for diagonal cells
+ for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++)
{
double cell = Math.pow(hValues[diagonalIndex], 2);
- eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell);
- estimatedPositions.add(new int[]{diagonalIndex, diagonalIndex});
+ eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell);
+ estimatedPositions.add(new int[] { diagonalIndex, diagonalIndex });
}
- /*Refine total values of each h_i:
- *Initialise h_values of the hypothetical non-existant previous iteration
- *with the correct format but with impossible values.
- Needed for exit condition of otherwise endless loop.*/
- System.out.print("initial values: [ ");
- for (double h : hValues)
- {
- System.out.print(String.format("%1.4f, ", h));
- }
- System.out.println(" ]");
-
-
- double[] hValuesOld = new double[matrixWidth];
-
- int iterationCount = 0;
-
- // repeat unitl values of h do not significantly change anymore
- while (true)
- {
- for (int hIndex = 0; hIndex < matrixWidth; hIndex++)
- {
- double newH = Arrays.stream(MiscMath.elementwiseMultiply(hValues, eigenMatrix.getRow(hIndex))).sum() / Arrays.stream(MiscMath.elementwiseMultiply(hValues, hValues)).sum();
- hValues[hIndex] = newH;
- }
-
- System.out.print(String.format("iteration %d: [ ", iterationCount));
+ /*Refine total values of each h_i:
+ *Initialise h_values of the hypothetical non-existant previous iteration
+ *with the correct format but with impossible values.
+ Needed for exit condition of otherwise endless loop.*/
+ System.out.print("initial values: [ ");
for (double h : hValues)
{
- System.out.print(String.format("%1.4f, ", h));
+ System.out.print(String.format("%1.4f, ", h));
}
System.out.println(" ]");
- //update values of estimated positions
- for (int[] pair : estimatedPositions) // pair ~ row, col
- {
- double newVal = hValues[pair[0]] * hValues[pair[1]];
- eigenMatrix.setValue(pair[0], pair[1], newVal);
- eigenMatrix.setValue(pair[1], pair[0], newVal);
- }
+ double[] hValuesOld = new double[matrixWidth];
- iterationCount++;
+ int iterationCount = 0;
- //exit loop as soon as new values are similar to the last iteration
- if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false))
+ // repeat unitl values of h do not significantly change anymore
+ while (true)
{
- break;
+ for (int hIndex = 0; hIndex < matrixWidth; hIndex++)
+ {
+ double newH = Arrays
+ .stream(MiscMath.elementwiseMultiply(hValues,
+ eigenMatrix.getRow(hIndex)))
+ .sum()
+ / Arrays.stream(
+ MiscMath.elementwiseMultiply(hValues, hValues))
+ .sum();
+ hValues[hIndex] = newH;
+ }
+
+ System.out.print(String.format("iteration %d: [ ", iterationCount));
+ for (double h : hValues)
+ {
+ System.out.print(String.format("%1.4f, ", h));
+ }
+ System.out.println(" ]");
+
+ // update values of estimated positions
+ for (int[] pair : estimatedPositions) // pair ~ row, col
+ {
+ double newVal = hValues[pair[0]] * hValues[pair[1]];
+ eigenMatrix.setValue(pair[0], pair[1], newVal);
+ eigenMatrix.setValue(pair[1], pair[0], newVal);
+ }
+
+ iterationCount++;
+
+ // exit loop as soon as new values are similar to the last iteration
+ if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false))
+ {
+ break;
+ }
+
+ // save hValues for comparison in the next iteration
+ System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length);
}
- //save hValues for comparison in the next iteration
- System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length);
- }
-
- //-----------------------------
- //Use complemented symmetric matrix to calculate final representative
- //vectors.
-
- //Eigendecomposition.
- eigenMatrix.tred();
- eigenMatrix.tqli();
+ // -----------------------------
+ // Use complemented symmetric matrix to calculate final representative
+ // vectors.
- System.out.println("eigenmatrix");
- eigenMatrix.print(System.out, "%8.2f");
- System.out.println();
- System.out.println("uncorrected eigenvalues");
- eigenMatrix.printD(System.out, "%2.4f ");
- System.out.println();
+ // Eigendecomposition.
+ eigenMatrix.tred();
+ eigenMatrix.tqli();
- double[] eigenVals = eigenMatrix.getD();
+ System.out.println("eigenmatrix");
+ eigenMatrix.print(System.out, "%8.2f");
+ System.out.println();
+ System.out.println("uncorrected eigenvalues");
+ eigenMatrix.printD(System.out, "%2.4f ");
+ System.out.println();
- TreeMap<Double, Integer> eigenPairs = new TreeMap<>(Comparator.reverseOrder());
- for (int i = 0; i < eigenVals.length; i++)
- {
- eigenPairs.put(eigenVals[i], i);
- }
+ double[] eigenVals = eigenMatrix.getD();
- // matrix of representative eigenvectors (each row is a vector)
- double[][] _repMatrix = new double[eigenVals.length][dim];
- double[][] _oldMatrix = new double[eigenVals.length][dim];
- double[] correctedEigenValues = new double[dim];
-
- int l = 0;
- for (Entry<Double, Integer> pair : eigenPairs.entrySet())
- {
- double eigenValue = pair.getKey();
- int column = pair.getValue();
- double[] eigenVector = eigenMatrix.getColumn(column);
- //for 2nd and higher eigenvalues
- if (l >= 1)
+ TreeMap<Double, Integer> eigenPairs = new TreeMap<>(
+ Comparator.reverseOrder());
+ for (int i = 0; i < eigenVals.length; i++)
{
- eigenValue /= correctionFactor;
+ eigenPairs.put(eigenVals[i], i);
}
- correctedEigenValues[l] = eigenValue;
- for (int j = 0; j < eigenVector.length; j++)
- {
- _repMatrix[j][l] = (eigenValue < 0) ? 0.0 : - Math.sqrt(eigenValue) * eigenVector[j];
- double tmpOldScore = scoresOld.getColumn(column)[j];
- _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0 : tmpOldScore;
- }
- l++;
- if (l >= dim)
- {
- break;
- }
- }
- System.out.println("correctedEigenValues");
- MiscMath.print(correctedEigenValues, "%2.4f ");
-
- repMatrix = new Matrix(_repMatrix);
- repMatrix.setD(correctedEigenValues);
- MatrixI oldMatrix = new Matrix(_oldMatrix);
-
- MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
-
- double rmsd = scoresOld.rmsd(dotMatrix);
-
- System.out.println("iteration, rmsd, maxDiff, rmsdDiff");
- System.out.println(String.format("0, %8.5f, -, -", rmsd));
- // Refine representative vectors by minimising sum-of-squared deviates between dotMatrix and original score matrix
- for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to 20
- {
- MatrixI repMatrixOLD = repMatrix.copy();
- MatrixI dotMatrixOLD = dotMatrix.copy();
+ // matrix of representative eigenvectors (each row is a vector)
+ double[][] _repMatrix = new double[eigenVals.length][dim];
+ double[][] _oldMatrix = new double[eigenVals.length][dim];
+ double[] correctedEigenValues = new double[dim];
- // for all rows/hA in the original matrix
- for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++)
+ int l = 0;
+ for (Entry<Double, Integer> pair : eigenPairs.entrySet())
{
- double[] row = oldMatrix.getRow(hAIndex);
- double[] hA = repMatrix.getRow(hAIndex);
- hAIndex = hAIndex;
- //find least-squares-solution fo rdifferences between original scores and representative vectors
- double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld, hAIndex);
- // update repMatrix with new hAlsm
- for (int j = 0; j < repMatrix.width(); j++)
- {
- repMatrix.setValue(hAIndex, j, hAlsm[j]);
- }
- }
-
- // dot product of representative vecotrs yields a matrix with values approximating the correlation matrix
- dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
- // calculate rmsd between approximation and correlation matrix
- rmsd = scoresOld.rmsd(dotMatrix);
-
- // calculate maximum change of representative vectors of current iteration
- MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute();
- double maxDiff = 0.0;
- for (int i = 0; i < diff.height(); i++)
- {
- for (int j = 0; j < diff.width(); j++)
- {
- maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j) : maxDiff;
- }
+ double eigenValue = pair.getKey();
+ int column = pair.getValue();
+ double[] eigenVector = eigenMatrix.getColumn(column);
+ // for 2nd and higher eigenvalues
+ if (l >= 1)
+ {
+ eigenValue /= correctionFactor;
+ }
+ correctedEigenValues[l] = eigenValue;
+ for (int j = 0; j < eigenVector.length; j++)
+ {
+ _repMatrix[j][l] = (eigenValue < 0) ? 0.0
+ : -Math.sqrt(eigenValue) * eigenVector[j];
+ double tmpOldScore = scoresOld.getColumn(column)[j];
+ _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0
+ : tmpOldScore;
+ }
+ l++;
+ if (l >= dim)
+ {
+ break;
+ }
}
- // calculate rmsd between current and previous estimation
- double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD);
+ System.out.println("correctedEigenValues");
+ MiscMath.print(correctedEigenValues, "%2.4f ");
+
+ repMatrix = new Matrix(_repMatrix);
+ repMatrix.setD(correctedEigenValues);
+ MatrixI oldMatrix = new Matrix(_oldMatrix);
- System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f", iteration, rmsd, maxDiff, rmsdDiff));
+ MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
- if (!(Math.abs(maxDiff) > 1e-06))
+ double rmsd = scoresOld.rmsd(dotMatrix);
+
+ System.out.println("iteration, rmsd, maxDiff, rmsdDiff");
+ System.out.println(String.format("0, %8.5f, -, -", rmsd));
+ // Refine representative vectors by minimising sum-of-squared deviates
+ // between dotMatrix and original score matrix
+ for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to
+ // 20
{
- repMatrix = repMatrixOLD.copy();
- break;
+ MatrixI repMatrixOLD = repMatrix.copy();
+ MatrixI dotMatrixOLD = dotMatrix.copy();
+
+ // for all rows/hA in the original matrix
+ for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++)
+ {
+ double[] row = oldMatrix.getRow(hAIndex);
+ double[] hA = repMatrix.getRow(hAIndex);
+ hAIndex = hAIndex;
+ // find least-squares-solution fo rdifferences between original scores
+ // and representative vectors
+ double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld,
+ hAIndex);
+ // update repMatrix with new hAlsm
+ for (int j = 0; j < repMatrix.width(); j++)
+ {
+ repMatrix.setValue(hAIndex, j, hAlsm[j]);
+ }
+ }
+
+ // dot product of representative vecotrs yields a matrix with values
+ // approximating the correlation matrix
+ dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
+ // calculate rmsd between approximation and correlation matrix
+ rmsd = scoresOld.rmsd(dotMatrix);
+
+ // calculate maximum change of representative vectors of current
+ // iteration
+ MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute();
+ double maxDiff = 0.0;
+ for (int i = 0; i < diff.height(); i++)
+ {
+ for (int j = 0; j < diff.width(); j++)
+ {
+ maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j)
+ : maxDiff;
+ }
+ }
+
+ // calculate rmsd between current and previous estimation
+ double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD);
+
+ System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f",
+ iteration, rmsd, maxDiff, rmsdDiff));
+
+ if (!(Math.abs(maxDiff) > 1e-06))
+ {
+ repMatrix = repMatrixOLD.copy();
+ break;
+ }
}
- }
-
} catch (Exception q)
{
}
/**
- * Create equations system using information on originally known
- * pairwise correlation coefficients (parsed from infile) and the
- * representative result vectors
- *
- * Each equation has the format:
- * hA * hA - pairwiseCC = 0
- * with:
- * hA: unknown variable
- * hB: known representative vector
- * pairwiseCC: known pairwise correlation coefficien
- *
- * The resulting equations system is overdetermined, if there are more
- * equations than unknown elements
- *
- * @param x ~ unknown n-dimensional column-vector
- * (needed for generating equations system, NOT to be specified by user).
- * @param hAIndex ~ index of currently optimised representative result vector.
- * @param h ~ matrix with row-wise listing of representative result vectors.
- * @param originalRow ~ matrix-row of originally parsed pairwise correlation coefficients.
- *
- * @return
- */
- private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
+ * Create equations system using information on originally known pairwise
+ * correlation coefficients (parsed from infile) and the representative result
+ * vectors
+ *
+ * Each equation has the format: hA * hA - pairwiseCC = 0 with: hA: unknown
+ * variable hB: known representative vector pairwiseCC: known pairwise
+ * correlation coefficien
+ *
+ * The resulting equations system is overdetermined, if there are more
+ * equations than unknown elements
+ *
+ * @param x
+ * ~ unknown n-dimensional column-vector (needed for generating
+ * equations system, NOT to be specified by user).
+ * @param hAIndex
+ * ~ index of currently optimised representative result vector.
+ * @param h
+ * ~ matrix with row-wise listing of representative result vectors.
+ * @param originalRow
+ * ~ matrix-row of originally parsed pairwise correlation
+ * coefficients.
+ *
+ * @return
+ */
+ private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix,
+ MatrixI scoresOld, int hAIndex)
{
double[] originalRow = scoresOld.getRow(hAIndex);
int nans = MiscMath.countNaN(originalRow);
double[] result = new double[originalRow.length - nans];
- //for all pairwiseCC in originalRow
+ // for all pairwiseCC in originalRow
int resultIndex = 0;
for (int hBIndex = 0; hBIndex < originalRow.length; hBIndex++)
{
if (!Double.isNaN(pairwiseCC))
{
double[] hB = repMatrix.getRow(hBIndex);
- result[resultIndex++] = MiscMath.sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC;
- } else {
+ result[resultIndex++] = MiscMath
+ .sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC;
+ }
+ else
+ {
}
}
return result;
}
/**
- * returns the jacobian matrix
- * @param repMatrix ~ matrix of representative vectors
- * @param hAIndex ~ current row index
- *
- * @return
- */
- private MatrixI approximateDerivative(MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
+ * returns the jacobian matrix
+ *
+ * @param repMatrix
+ * ~ matrix of representative vectors
+ * @param hAIndex
+ * ~ current row index
+ *
+ * @return
+ */
+ private MatrixI approximateDerivative(MatrixI repMatrix,
+ MatrixI scoresOld, int hAIndex)
{
- //hA = x0
+ // hA = x0
double[] hA = repMatrix.getRow(hAIndex);
- double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, hAIndex);
+ double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld,
+ hAIndex);
double[] signX0 = new double[hA.length];
double[] xAbs = new double[hA.length];
for (int i = 0; i < hA.length; i++)
{
signX0[i] = (hA[i] >= 0) ? 1 : -1;
xAbs[i] = (Math.abs(hA[i]) >= 1.0) ? Math.abs(hA[i]) : 1.0;
- }
+ }
double rstep = Math.pow(Math.ulp(1.0), 0.5);
- double[] h = new double [hA.length];
+ double[] h = new double[hA.length];
for (int i = 0; i < hA.length; i++)
{
h[i] = rstep * signX0[i] * xAbs[i];
}
-
+
int m = f0.length;
int n = hA.length;
double[][] jTransposed = new double[n][m];
System.arraycopy(hA, 0, x, 0, h.length);
x[i] += h[i];
double dx = x[i] - hA[i];
- double[] df = originalToEquasionSystem(x, repMatrix, scoresOld, hAIndex);
+ double[] df = originalToEquasionSystem(x, repMatrix, scoresOld,
+ hAIndex);
for (int j = 0; j < df.length; j++)
{
- df[j] -= f0[j];
- jTransposed[i][j] = df[j] / dx;
+ df[j] -= f0[j];
+ jTransposed[i][j] = df[j] / dx;
}
}
MatrixI J = new Matrix(jTransposed).transpose();
}
/**
- * norm of regularized (by alpha) least-squares solution minus Delta
- * @param alpha
- * @param suf
- * @param s
- * @param Delta
- *
- * @return
- */
- private double[] phiAndDerivative(double alpha, double[] suf, double[] s, double Delta)
+ * norm of regularized (by alpha) least-squares solution minus Delta
+ *
+ * @param alpha
+ * @param suf
+ * @param s
+ * @param Delta
+ *
+ * @return
+ */
+ private double[] phiAndDerivative(double alpha, double[] suf, double[] s,
+ double Delta)
{
- double[] denom = MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha);
+ double[] denom = MiscMath
+ .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha);
double pNorm = MiscMath.norm(MiscMath.elementwiseDivide(suf, denom));
double phi = pNorm - Delta;
// - sum ( suf**2 / denom**3) / pNorm
- double phiPrime = - MiscMath.sum(MiscMath.elementwiseDivide(MiscMath.elementwiseMultiply(suf, suf), MiscMath.elementwiseMultiply(MiscMath.elementwiseMultiply(denom, denom), denom))) / pNorm;
- return new double[]{phi, phiPrime};
+ double phiPrime = -MiscMath.sum(MiscMath.elementwiseDivide(
+ MiscMath.elementwiseMultiply(suf, suf),
+ MiscMath.elementwiseMultiply(
+ MiscMath.elementwiseMultiply(denom, denom), denom)))
+ / pNorm;
+ return new double[] { phi, phiPrime };
}
/**
- * class holding the result of solveLsqTrustRegion
- */
+ * class holding the result of solveLsqTrustRegion
+ */
private class TrustRegion
{
private double[] step;
+
private double alpha;
+
private int iteration;
public TrustRegion(double[] step, double alpha, int iteration)
{
return this.alpha;
}
-
+
public int getIteration()
{
return this.iteration;
}
/**
- * solve a trust-region problem arising in least-squares optimisation
- * @param n ~ number of variables
- * @param m ~ number of residuals
- * @param uf
- * @param s ~ singular values of J
- * @param V ~ transpose of VT
- * @param Delta ~ radius of a trust region
- * @param alpha ~ initial guess for alpha
- *
- * @return
- */
- private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf, double[] s, MatrixI V, double Delta, double alpha)
+ * solve a trust-region problem arising in least-squares optimisation
+ *
+ * @param n
+ * ~ number of variables
+ * @param m
+ * ~ number of residuals
+ * @param uf
+ * @param s
+ * ~ singular values of J
+ * @param V
+ * ~ transpose of VT
+ * @param Delta
+ * ~ radius of a trust region
+ * @param alpha
+ * ~ initial guess for alpha
+ *
+ * @return
+ */
+ private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf,
+ double[] s, MatrixI V, double Delta, double alpha)
{
double[] suf = MiscMath.elementwiseMultiply(s, uf);
- //check if J has full rank and tr Gauss-Newton step
+ // check if J has full rank and tr Gauss-Newton step
boolean fullRank = false;
if (m >= n)
{
}
if (fullRank)
{
- double[] p = MiscMath.elementwiseMultiply(V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1);
+ double[] p = MiscMath.elementwiseMultiply(
+ V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1);
if (MiscMath.norm(p) <= Delta)
{
TrustRegion result = new TrustRegion(p, 0.0, 0);
if (fullRank)
{
double[] phiAndPrime = phiAndDerivative(0.0, suf, s, Delta);
- alphaLower = - phiAndPrime[0] / phiAndPrime[1];
+ alphaLower = -phiAndPrime[0] / phiAndPrime[1];
}
- alpha = (!fullRank && alpha == 0.0) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
+ alpha = (!fullRank && alpha == 0.0)
+ ? alpha = Math.max(0.001 * alphaUpper,
+ Math.pow(alphaLower * alphaUpper, 0.5))
+ : alpha;
int iteration = 0;
- while (iteration < 10) // 10 is default max_iter
+ while (iteration < 10) // 10 is default max_iter
{
- alpha = (alpha < alphaLower || alpha > alphaUpper) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
+ alpha = (alpha < alphaLower || alpha > alphaUpper)
+ ? alpha = Math.max(0.001 * alphaUpper,
+ Math.pow(alphaLower * alphaUpper, 0.5))
+ : alpha;
double[] phiAndPrime = phiAndDerivative(alpha, suf, s, Delta);
double phi = phiAndPrime[0];
double phiPrime = phiAndPrime[1];
alphaLower = Math.max(alphaLower, alpha - ratio);
alpha -= (phi + Delta) * ratio / Delta;
- if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01
+ if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01
{
- break;
+ break;
}
iteration++;
}
// p = - V.dot( suf / (s**2 + alpha))
- double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha));
+ double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath
+ .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha));
double[] p = MiscMath.elementwiseMultiply(V.sumProduct(tmp), -1);
- // Make the norm of p equal to Delta, p is changed only slightly during this.
+ // Make the norm of p equal to Delta, p is changed only slightly during
+ // this.
// It is done to prevent p lie outside of the trust region
p = MiscMath.elementwiseMultiply(p, Delta / MiscMath.norm(p));
}
/**
- * compute values of a quadratic function arising in least squares
- * function: 0.5 * s.T * (J.T * J + diag) * s + g.T * s
- *
- * @param J ~ jacobian matrix
- * @param g ~ gradient
- * @param s ~ steps and rows
- *
- * @return
- */
+ * compute values of a quadratic function arising in least squares function:
+ * 0.5 * s.T * (J.T * J + diag) * s + g.T * s
+ *
+ * @param J
+ * ~ jacobian matrix
+ * @param g
+ * ~ gradient
+ * @param s
+ * ~ steps and rows
+ *
+ * @return
+ */
private double evaluateQuadratic(MatrixI J, double[] g, double[] s)
{
}
/**
- * update the radius of a trust region based on the cost reduction
- *
- * @param Delta
- * @param actualReduction
- * @param predictedReduction
- * @param stepNorm
- * @param boundHit
- *
- * @return
- */
- private double[] updateTrustRegionRadius(double Delta, double actualReduction, double predictedReduction, double stepNorm, boolean boundHit)
+ * update the radius of a trust region based on the cost reduction
+ *
+ * @param Delta
+ * @param actualReduction
+ * @param predictedReduction
+ * @param stepNorm
+ * @param boundHit
+ *
+ * @return
+ */
+ private double[] updateTrustRegionRadius(double Delta,
+ double actualReduction, double predictedReduction,
+ double stepNorm, boolean boundHit)
{
double ratio = 0;
if (predictedReduction > 0)
{
ratio = actualReduction / predictedReduction;
- } else if (predictedReduction == 0 && actualReduction == 0) {
+ }
+ else if (predictedReduction == 0 && actualReduction == 0)
+ {
ratio = 1;
- } else {
+ }
+ else
+ {
ratio = 0;
}
if (ratio < 0.25)
{
Delta = 0.25 * stepNorm;
- } else if (ratio > 0.75 && boundHit) {
+ }
+ else if (ratio > 0.75 && boundHit)
+ {
Delta *= 2.0;
}
- return new double[]{Delta, ratio};
+ return new double[] { Delta, ratio };
}
/**
- * trust region reflective algorithm
- * @param repMatrix ~ Matrix containing representative vectors
- * @param scoresOld ~ Matrix containing initial observations
- * @param index ~ current row index
- * @param J ~ jacobian matrix
- *
- * @return
- */
- private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index, MatrixI J)
+ * trust region reflective algorithm
+ *
+ * @param repMatrix
+ * ~ Matrix containing representative vectors
+ * @param scoresOld
+ * ~ Matrix containing initial observations
+ * @param index
+ * ~ current row index
+ * @param J
+ * ~ jacobian matrix
+ *
+ * @return
+ */
+ private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index,
+ MatrixI J)
{
- //hA = x0
+ // hA = x0
double[] hA = repMatrix.getRow(index);
double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, index);
int nfev = 1;
double[] g = J.transpose().sumProduct(f0);
double Delta = MiscMath.norm(hA);
int maxNfev = hA.length * 100;
- double alpha = 0.0; // "Levenberg-Marquardt" parameter
+ double alpha = 0.0; // "Levenberg-Marquardt" parameter
double gNorm = 0;
boolean terminationStatus = false;
gNorm = MiscMath.norm(g);
if (terminationStatus || nfev == maxNfev)
{
- break;
+ break;
}
- SingularValueDecomposition svd = new SingularValueDecomposition(new Array2DRowRealMatrix(J.asArray()));
+ SingularValueDecomposition svd = new SingularValueDecomposition(
+ new Array2DRowRealMatrix(J.asArray()));
MatrixI U = new Matrix(svd.getU().getData());
- double[] s = svd.getSingularValues();
+ double[] s = svd.getSingularValues();
MatrixI V = new Matrix(svd.getV().getData()).transpose();
double[] uf = U.transpose().sumProduct(f0);
double[] fNew = new double[f0.length];
double costNew = 0;
double stepHnorm = 0;
-
+
while (actualReduction <= 0 && nfev < maxNfev)
{
- TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta, alpha);
- double[] stepH = trustRegion.getStep();
- alpha = trustRegion.getAlpha();
- int nIterations = trustRegion.getIteration();
- double predictedReduction = - (evaluateQuadratic(J, g, stepH));
+ TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta,
+ alpha);
+ double[] stepH = trustRegion.getStep();
+ alpha = trustRegion.getAlpha();
+ int nIterations = trustRegion.getIteration();
+ double predictedReduction = -(evaluateQuadratic(J, g, stepH));
xNew = MiscMath.elementwiseAdd(hA, stepH);
- fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index);
- nfev++;
-
- stepHnorm = MiscMath.norm(stepH);
+ fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index);
+ nfev++;
- if (MiscMath.countNaN(fNew) > 0)
- {
- Delta = 0.25 * stepHnorm;
- continue;
- }
+ stepHnorm = MiscMath.norm(stepH);
- // usual trust-region step quality estimation
- costNew = 0.5 * MiscMath.dot(fNew, fNew);
- actualReduction = cost - costNew;
+ if (MiscMath.countNaN(fNew) > 0)
+ {
+ Delta = 0.25 * stepHnorm;
+ continue;
+ }
- double[] updatedTrustRegion = updateTrustRegionRadius(Delta, actualReduction, predictedReduction, stepHnorm, stepHnorm > (0.95 * Delta));
- double DeltaNew = updatedTrustRegion[0];
- double ratio = updatedTrustRegion[1];
+ // usual trust-region step quality estimation
+ costNew = 0.5 * MiscMath.dot(fNew, fNew);
+ actualReduction = cost - costNew;
- // default ftol and xtol = 1e-8
- boolean ftolSatisfied = actualReduction < (1e-8 * cost) && ratio > 0.25;
- boolean xtolSatisfied = stepHnorm < (1e-8 * (1e-8 + MiscMath.norm(hA)));
- terminationStatus = ftolSatisfied || xtolSatisfied;
- if (terminationStatus)
- {
- break;
- }
+ double[] updatedTrustRegion = updateTrustRegionRadius(Delta,
+ actualReduction, predictedReduction, stepHnorm,
+ stepHnorm > (0.95 * Delta));
+ double DeltaNew = updatedTrustRegion[0];
+ double ratio = updatedTrustRegion[1];
- alpha *= Delta / DeltaNew;
- Delta = DeltaNew;
+ // default ftol and xtol = 1e-8
+ boolean ftolSatisfied = actualReduction < (1e-8 * cost)
+ && ratio > 0.25;
+ boolean xtolSatisfied = stepHnorm < (1e-8
+ * (1e-8 + MiscMath.norm(hA)));
+ terminationStatus = ftolSatisfied || xtolSatisfied;
+ if (terminationStatus)
+ {
+ break;
+ }
+
+ alpha *= Delta / DeltaNew;
+ Delta = DeltaNew;
}
if (actualReduction > 0)
{
- hA = xNew;
- f0 = fNew;
- cost = costNew;
+ hA = xNew;
+ f0 = fNew;
+ cost = costNew;
- J = approximateDerivative(repMatrix, scoresOld, index);
+ J = approximateDerivative(repMatrix, scoresOld, index);
g = J.transpose().sumProduct(f0);
- } else {
+ }
+ else
+ {
stepHnorm = 0;
- actualReduction = 0;
+ actualReduction = 0;
}
iteration++;
}
}
/**
- * performs the least squares optimisation
- * adapted from https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares
- *
- * @param repMatrix ~ Matrix containing representative vectors
- * @param scoresOld ~ Matrix containing initial observations
- * @param index ~ current row index
- *
- * @return
- */
- private double[] leastSquaresOptimisation(MatrixI repMatrix, MatrixI scoresOld, int index)
+ * performs the least squares optimisation adapted from
+ * https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares
+ *
+ * @param repMatrix
+ * ~ Matrix containing representative vectors
+ * @param scoresOld
+ * ~ Matrix containing initial observations
+ * @param index
+ * ~ current row index
+ *
+ * @return
+ */
+ private double[] leastSquaresOptimisation(MatrixI repMatrix,
+ MatrixI scoresOld, int index)
{
MatrixI J = approximateDerivative(repMatrix, scoresOld, index);
double[] result = trf(repMatrix, scoresOld, index, J);
return similarities;
}
-
+
}
public boolean isProtein()
{
return true;
- }
+ }
@Override
public String toString()
private final ScoreMatrix PAM250;
private final ScoreMatrix DNA;
-
+
private final ScoreMatrix SECONDARYSTRUCTURE;
private static ScoreModels instance;
* <li>PAM250</li>
* <li>PID</li>
* <li>DNA</li>
- * <li>Sequence Feature Similarity</li> *
+ * <li>Sequence Feature Similarity</li> *
* <li>Secondary Structure Similarity</li>
* </ul>
*/
DNA = loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
- SECONDARYSTRUCTURE = loadScoreMatrix("scoreModel/secondarystructure.scm");
- registerScoreModel(new SecondaryStructureDistanceModel());
+ SECONDARYSTRUCTURE = loadScoreMatrix(
+ "scoreModel/secondarystructure.scm");
+ registerScoreModel(new SecondaryStructureDistanceModel());
}
public void registerScoreModel(ScoreModelI sm)
{
- if(sm.getName().equals("SECONDARYSTRUCTURE")) {
+ if (sm.getName().equals("SECONDARYSTRUCTURE"))
+ {
return;
}
ScoreModelI sm2 = models.get(sm.getName());
{
return PAM250;
}
-
+
public ScoreMatrix getSecondaryStructureMatrix()
{
return SECONDARYSTRUCTURE;
private static final String NAME = "Secondary Structure Similarity";
private ScoreMatrix ssRateMatrix;
-
- private String description;
-
+
+ private String description;
+
FeatureRenderer fr;
-
-
+
/**
* Constructor
*/
public SecondaryStructureDistanceModel()
{
-
+
}
-
+
@Override
public ScoreModelI getInstance(AlignmentViewPanel view)
{
fr = view.cloneFeatureRenderer();
return true;
}
-
+
ArrayList<AlignmentAnnotation> ssForSeqs = null;
@Override
public SequenceI[] expandSeqData(SequenceI[] sequences,
- AlignmentView seqData, SimilarityParamsI scoreParams,List<String> labels)
+ AlignmentView seqData, SimilarityParamsI scoreParams,
+ List<String> labels)
{
ssForSeqs = new ArrayList<AlignmentAnnotation>();
List<SequenceI> newSequences = new ArrayList<SequenceI>();
List<SeqCigar> newCigs = new ArrayList<SeqCigar>();
int sq = 0;
-
-
AlignmentAnnotation[] alignAnnotList = fr.getViewport().getAlignment()
- .getAlignmentAnnotation();
-
- String ssSource = scoreParams.getSecondaryStructureSource();
- if(ssSource == null || ssSource == "") {
+ .getAlignmentAnnotation();
+
+ String ssSource = scoreParams.getSecondaryStructureSource();
+ if (ssSource == null || ssSource == "")
+ {
ssSource = Constants.SS_ALL_PROVIDERS;
}
-
+
/*
* Add secondary structure annotations that are added to the annotation track
* to the map
*/
- Map<SequenceI, ArrayList<AlignmentAnnotation>> ssAlignmentAnnotationForSequences
- = AlignmentUtils.getSequenceAssociatedAlignmentAnnotations(alignAnnotList, ssSource);
-
+ Map<SequenceI, ArrayList<AlignmentAnnotation>> ssAlignmentAnnotationForSequences = AlignmentUtils
+ .getSequenceAssociatedAlignmentAnnotations(alignAnnotList,
+ ssSource);
+
for (SeqCigar scig : seqData.getSequences())
{
// get the next sequence that should be bound to this scig: may be null
SequenceI alSeq = sequences[sq++];
- List<AlignmentAnnotation> ssec = ssAlignmentAnnotationForSequences.get(scig.getRefSeq());
+ List<AlignmentAnnotation> ssec = ssAlignmentAnnotationForSequences
+ .get(scig.getRefSeq());
if (ssec == null)
{
// not defined
newSequences.add(alSeq);
- if (alSeq!=null) {
+ if (alSeq != null)
+ {
labels.add("No Secondary Structure");
}
- SeqCigar newSeqCigar = scig; //new SeqCigar(scig);
+ SeqCigar newSeqCigar = scig; // new SeqCigar(scig);
newCigs.add(newSeqCigar);
ssForSeqs.add(null);
- } else {
+ }
+ else
+ {
for (int i = 0; i < ssec.size(); i++)
{
if (alSeq != null)
labels.add(AlignmentUtils
.extractSSSourceFromAnnotationDescription(ssec.get(i)));
}
- //newSequences.add(seq);
+ // newSequences.add(seq);
newSequences.add(alSeq);
SeqCigar newSeqCigar = scig; // new SeqCigar(scig);
newCigs.add(newSeqCigar);
}
/**
- * Calculates distance score [i][j] between each pair of protein sequences
- * based on their secondary structure annotations (H, E, C).
- * The final score is normalised by the number of
- * alignment columns processed, providing an average similarity score.
+ * Calculates distance score [i][j] between each pair of protein sequences
+ * based on their secondary structure annotations (H, E, C). The final score
+ * is normalised by the number of alignment columns processed, providing an
+ * average similarity score.
* <p>
- * The parameters argument can include settings for handling gap-residue aligned
- * positions and may determine if the score calculation is based on the longer or shorter
- * sequence in each pair. This can be important for handling partial alignments or
- * sequences of significantly different lengths.
+ * The parameters argument can include settings for handling gap-residue
+ * aligned positions and may determine if the score calculation is based on
+ * the longer or shorter sequence in each pair. This can be important for
+ * handling partial alignments or sequences of significantly different
+ * lengths.
*
- * @param seqData The aligned sequence data including secondary structure annotations.
- * @param params Additional parameters for customising the scoring process, such as gap
- * handling and sequence length consideration.
+ * @param seqData
+ * The aligned sequence data including secondary structure
+ * annotations.
+ * @param params
+ * Additional parameters for customising the scoring process, such as
+ * gap handling and sequence length consideration.
*/
@Override
public MatrixI findDistances(AlignmentView seqData,
SimilarityParamsI params)
- {
- if (ssForSeqs==null || ssForSeqs.size()!=seqData.getSequences().length)
+ {
+ if (ssForSeqs == null
+ || ssForSeqs.size() != seqData.getSequences().length)
{
// expandSeqData needs to be called to initialise the hash
SequenceI[] sequences = new SequenceI[seqData.getSequences().length];
expandSeqData(sequences, seqData, params, new ArrayList<String>());
}
SeqCigar[] seqs = seqData.getSequences();
- int noseqs = seqs.length; //no of sequences
- int cpwidth = 0;
- double[][] similarities = new double[noseqs][noseqs]; //matrix to store similarity score
- //secondary structure source parameter selected by the user from the drop down.
- String ssSource = params.getSecondaryStructureSource();
- if(ssSource == null || ssSource == "") {
+ int noseqs = seqs.length; // no of sequences
+ int cpwidth = 0;
+ double[][] similarities = new double[noseqs][noseqs]; // matrix to store
+ // similarity score
+ // secondary structure source parameter selected by the user from the drop
+ // down.
+ String ssSource = params.getSecondaryStructureSource();
+ if (ssSource == null || ssSource == "")
+ {
ssSource = Constants.SS_ALL_PROVIDERS;
}
ssRateMatrix = ScoreModels.getInstance().getSecondaryStructureMatrix();
-
+
// need to get real position for view position
int[] viscont = seqData.getVisibleContigs();
-
-
/*
* scan each column, compute and add to each similarity[i, j]
*/
for (int vc = 0; vc < viscont.length; vc += 2)
{
- //Iterates for each column position
- for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
+ // Iterates for each column position
+ for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
{
- cpwidth++; //used to normalise the similarity score
+ cpwidth++; // used to normalise the similarity score
/*
* get set of sequences without gap in the current column
*/
- Set<SeqCigar> seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs, cpos);
+ Set<SeqCigar> seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs,
+ cpos);
/*
* calculate similarity score for each secondary structure annotation on i'th and j'th
* and fill in the bottom half of the matrix
*/
// TODO JAL-2424 cpwidth may be out by 1 - affects scores but not tree shape
-
+
for (int i = 0; i < noseqs; i++)
{
for (int j = i + 1; j < noseqs; j++)
- {
+ {
similarities[i][j] /= cpwidth;
similarities[j][i] = similarities[i][j];
}
}
- return SimilarityScoreModel.similarityToDistance(new Matrix(similarities));
-
+ return SimilarityScoreModel
+ .similarityToDistance(new Matrix(similarities));
+
}
/**
- * Builds and returns a set containing sequences (SeqCigar) which do not
- * have a gap at the given column position.
+ * Builds and returns a set containing sequences (SeqCigar) which do not have
+ * a gap at the given column position.
*
* @param seqs
* @param columnPosition
* (0..)
* @return
*/
- private Set<SeqCigar> findSeqsWithoutGapAtColumn(
- SeqCigar[] seqs, int columnPosition)
+ private Set<SeqCigar> findSeqsWithoutGapAtColumn(SeqCigar[] seqs,
+ int columnPosition)
{
Set<SeqCigar> seqsWithoutGapAtCol = new HashSet<>();
for (SeqCigar seq : seqs)
{
/*
* position is not a gap
- */
+ */
seqsWithoutGapAtCol.add(seq);
}
}
return seqsWithoutGapAtCol;
}
-
@Override
public String getName()
{
@Override
public boolean isDNA()
{
- return false;
+ return false;
}
@Override
{
return false;
}
-
+
@Override
public boolean isSecondaryStructure()
{
private boolean includeGaps;
private boolean denominateByShortestLength;
-
+
private String secondaryStructureSource;
/**
/**
* Justify alignment or currently selected region left or right
- * @param left - true - means justify left
+ *
+ * @param left
+ * - true - means justify left
* @return
*/
boolean justify_Region(boolean left);
boolean isValidCharWidth();
boolean isShowConsensusHistogram();
-
+
boolean isShowSequenceLogo();
-
+
boolean isNormaliseSequenceLogo();
ColourSchemeI getGlobalColourScheme();
* @return
*/
AlignmentAnnotation getAlignmentConsensusAnnotation();
-
- List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation();
+ List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation();
/**
* get the container for alignment gap annotation
* @param hconsensus
*/
void setSequenceConsensusHash(ProfilesI hconsensus);
-
- void setSequenceSSConsensusHash(Map<String, ProfilesI> hSSConsesnusProfileMap);
-
+
+ void setSequenceSSConsensusHash(
+ Map<String, ProfilesI> hSSConsesnusProfileMap);
/**
* Set the cDNA complement consensus for the viewport
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
/**
* notify all concerned that the alignment data has changed and derived data
* needs to be recalculated
public void notifyAlignmentChanged();
/**
- * retrieve a matrix associated with the view's alignment's annotation
+ * retrieve a matrix associated with the view's alignment's annotation
+ *
* @param alignmentAnnotation
* @return contact matrix or NULL
*/
boolean getColourAppliesToAllGroups();
boolean getAbovePIDThreshold();
-
+
boolean getByConsensusSecondaryStructureSelected();
void setIncrement(int inc);
boolean getScaleRightWrapped();
void setAbovePIDThreshold(boolean b);
-
+
void setByConsensusSecondaryStructureSelected(boolean b);
-
+
void setShowStructureProvider(boolean b);
boolean isShowStructureProvider();
// TODO getName, isDNA, isProtein can be static methods in Java 8
-
default public boolean isSecondaryStructure()
{
return false;
}
/**
- * Answers false by default
- * Answers true if the data has secondary structure (so should be
- * shown in menus in that context)
+ * Answers false by default Answers true if the data has secondary structure
+ * (so should be shown in menus in that context)
*
* @return
*/
-
-
+
/**
* Returns a distance score for the given sequence regions, that is, a matrix
* whose value [i][j] is the distance of sequence i from sequence j by some
ScoreModelI getInstance(AlignmentViewPanel avp);
/**
- * Score models may create multiple leaves for a single sequence - implement this method if you do
- * @param sequences - sequences to be filtered/expanded set of leaves
- * @param seqData - origin
- * @param labels - strings to show instead of the SequenceI.getName() for each element of sequences attached to leaves
+ * Score models may create multiple leaves for a single sequence - implement
+ * this method if you do
+ *
+ * @param sequences
+ * - sequences to be filtered/expanded set of leaves
+ * @param seqData
+ * - origin
+ * @param labels
+ * - strings to show instead of the SequenceI.getName() for each
+ * element of sequences attached to leaves
* @return filtered/expanded set of leaves to be analysed
*/
- default SequenceI[] expandSeqData(SequenceI[] sequences, AlignmentView seqData, SimilarityParamsI scoreParams, List<String> labels) {
- return sequences;
+ default SequenceI[] expandSeqData(SequenceI[] sequences,
+ AlignmentView seqData, SimilarityParamsI scoreParams,
+ List<String> labels)
+ {
+ return sequences;
};
}
* @return
*/
boolean denominateByShortestLength();
-
+
String getSecondaryStructureSource();
void setSecondaryStructureSource(String secondaryStructureSource);
Menu autoAnnMenu = new Menu(
MessageManager.getString("label.autocalculated_annotation"));
- Menu selectSS = new Menu(
- MessageManager.getString("label.select_secondary_structure_source"));
+ Menu selectSS = new Menu(MessageManager
+ .getString("label.select_secondary_structure_source"));
showGroupConsensus.addItemListener(this);
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null
- && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0,
- pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ for (int pdbsi = 0, pdbsiSize = pdbs
+ .size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
{
continue;
}
- char[] range = seq.getSequence(from, to+1);
- if (range==null || range.length==0)
+ char[] range = seq.getSequence(from, to + 1);
+ if (range == null || range.length == 0)
{
continue;
}
alseq[gapstart + gp] = gc;
}
- for (int sqp = 0,insp=0; sqp<alseq.length; sqp++)
+ for (int sqp = 0, insp = 0; sqp < alseq.length; sqp++)
{
if (sqp < range.length && !Comparison.isGap(range[sqp]))
{
// Technically we should return false, since view has not changed
return false;
}
-
+
@Override
public boolean justify_Region(boolean left)
{
public Hashtable alignmentProperties;
private List<AlignedCodonFrame> codonFrameList;
-
+
private void initAlignment(SequenceI[] seqs)
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
nucleotide = Comparison.isNucleotide(seqs);
sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
-
for (int i = 0; i < seqs.length; i++)
{
sequences.add(seqs[i]);
}
-
+
}
/**
public static final int CDNA_PROFILE = 2;
private static long counter = 0;
-
+
private long noOfSequencesIncluded = -1;
/**
String name;
- String label=null;
+ String label = null;
BinaryNode<T> left;
return oldstate;
}
+
/**
* check if there's a label to show
+ *
* @return true if non-empty/null string
*/
public boolean hasLabel()
{
- return label!=null && !label.isEmpty();
+ return label != null && !label.isEmpty();
}
+
public String getLabel()
{
return label;
public String getDisplayName()
{
- if (name!=null && !name.isBlank())
+ if (name != null && !name.isBlank())
{
-
- if (hasLabel()) {
- return getName()+"|"+label;
+
+ if (hasLabel())
+ {
+ return getName() + "|" + label;
}
return name;
}
- return hasLabel() ? label:"";
+ return hasLabel() ? label : "";
}
}
if (_hasProperty(AUTHORITATIVE_ID))
{
Object authId = getProperty(AUTHORITATIVE_ID);
- return (authId instanceof Boolean) ? (Boolean) authId : Boolean.valueOf(authId.toString());
+ return (authId instanceof Boolean) ? (Boolean) authId
+ : Boolean.valueOf(authId.toString());
}
return false;
}
public void setProviderCategory(String providerCategory)
{
- setProperty(PROVIDERCATEGORY, providerCategory);
+ setProperty(PROVIDERCATEGORY, providerCategory);
}
-
+
public String getProviderCategory()
{
return (String) getProperty(PROVIDERCATEGORY);
{
return _hasProperty(PROVIDERCATEGORY);
}
-
+
}
* an object holding counts of symbols in the profile
*/
private ResidueCount counts;
-
+
private SecondaryStructureCount ssCounts;
-
+
private int seqWithSSCount = -1;
/*
* the highest count for any residue in the profile
*/
private int maxCount;
+
private int maxSSCount;
-
/*
* the residue (e.g. K) or residues (e.g. KQW) with the
* highest count in the profile
*/
private String modalResidue;
-
+
private String modalSS;
/**
this.maxCount = max;
this.modalResidue = modalRes;
}
-
- public Profile(String modalSS, int ssCount, int gaps, int maxSSCount, int seqWithSSCount)
+
+ public Profile(String modalSS, int ssCount, int gaps, int maxSSCount,
+ int seqWithSSCount)
{
this.height = ssCount;
this.gapped = gaps;
{
this.counts = residueCounts;
}
-
+
@Override
public void setSSCounts(SecondaryStructureCount secondaryStructureCount)
{
}
return pid;
}
-
+
@Override
public float getSSPercentageIdentity(boolean ignoreGaps)
{
{
return counts;
}
-
+
@Override
public SecondaryStructureCount getSSCounts()
{
{
return maxCount;
}
-
+
@Override
public int getMaxSSCount()
{
{
return modalResidue;
}
-
+
@Override
public String getModalSS()
{
* @param residueCounts
*/
public abstract void setCounts(ResidueCount residueCounts);
- public abstract void setSSCounts(SecondaryStructureCount secondaryStructureCount);
-
+
+ public abstract void setSSCounts(
+ SecondaryStructureCount secondaryStructureCount);
/**
* Returns the percentage identity of the profile, i.e. the highest proportion
* @return
*/
public abstract float getPercentageIdentity(boolean ignoreGaps);
-
+
public abstract float getSSPercentageIdentity(boolean ignoreGaps);
/**
* @return
*/
public abstract int getHeight();
-
+
public abstract int getSeqWithSSCount();
/**
* @return
*/
public abstract int getMaxCount();
+
public abstract int getMaxSSCount();
/**
* @return
*/
public abstract String getModalResidue();
+
public abstract String getModalSS();
/**
* @return
*/
public abstract int getNonGapped();
+
SecondaryStructureCount getSSCounts();
}
\ No newline at end of file
*/
private static final String SS_SYMBOLS = "HEC";
-
static final int GAP_COUNT = 0;
/*
*/
public SecondaryStructureCount()
{
- //isSS = true;
+ // isSS = true;
int charsToCount = SS_SYMBOLS.length();
counts = new short[charsToCount + 1];
}
{
if (intCounts[i] == count)
{
- modal.append(
- SS_SYMBOLS.charAt(i - 1));
+ modal.append(SS_SYMBOLS.charAt(i - 1));
}
}
}
{
if (counts[i] == count)
{
- modal.append(
- SS_SYMBOLS.charAt(i - 1));
+ modal.append(SS_SYMBOLS.charAt(i - 1));
}
}
}
* consensus calculation property
*/
private boolean showSequenceLogo = false;
-
/**
* flag indicating if logo should be rendered normalised
private boolean hidecols = false;
AlignmentAnnotation consensus = null;
-
List<AlignmentAnnotation> ssConsensus = null;
-
+
List<String> secondaryStructureSources = null;
AlignmentAnnotation conservation = null;
private boolean showConsensusHistogram;
-
+
private AnnotatedCollectionI context;
-
+
public Map<String, ProfilesI> hSSConsensusProfileMap;
/**
}
return tmp.toArray(new SequenceI[tmp.size()]);
}
-
+
public List<String> getSecondaryStructureSources()
{
return secondaryStructureSources;
cs.setConsensus(cnsns);
upd = true;
}
-
+
hSSConsensusProfileMap = new HashMap<String, ProfilesI>();
- List <String> ssSources = new ArrayList<String>();
+ List<String> ssSources = new ArrayList<String>();
AnnotatedCollectionI aa = this.getContext();
-
- if(aa !=null )
+
+ if (aa != null)
{
- ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa.getAlignmentAnnotation());
+ ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(
+ aa.getAlignmentAnnotation());
}
- if(ssSources != null) {
+ if (ssSources != null)
+ {
ssSources.add(Constants.SS_ALL_PROVIDERS);
- for(String ssSource : ssSources) {
- ProfilesI hSSConsensus = AAFrequency.calculateSS(sequences, startRes, endRes + 1, showSequenceLogo,
- ssSource);
+ for (String ssSource : ssSources)
+ {
+ ProfilesI hSSConsensus = AAFrequency.calculateSS(sequences,
+ startRes, endRes + 1, showSequenceLogo, ssSource);
hSSConsensusProfileMap.put(ssSource, hSSConsensus);
}
}
-
if (ssConsensus != null)
{
_updateSSConsensusRow(hSSConsensusProfileMap, sequences.size());
upd = true;
}
-
+
if (cs != null)
{
cs.setSSConsensusProfileMap(hSSConsensusProfileMap);
upd = true;
}
-
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
// for
// ignoreGapsInConsensusCalculation);
}
-
-
+
/**
- * Updates the secondary structure consensus row based on the provided profiles map and the number of sequences.
+ * Updates the secondary structure consensus row based on the provided
+ * profiles map and the number of sequences.
*
- * @param hSSConsensusProfileMap A map containing secondary structure consensus profiles for each providers.
- * @param nseq The number of sequences.
+ * @param hSSConsensusProfileMap
+ * A map containing secondary structure consensus profiles for each
+ * providers.
+ * @param nseq
+ * The number of sequences.
*/
- private void _updateSSConsensusRow(Map<String, ProfilesI> hSSConsensusProfileMap, long nseq)
+ private void _updateSSConsensusRow(
+ Map<String, ProfilesI> hSSConsensusProfileMap, long nseq)
{
// Get a list of secondary structure sources from the profile map keys
- List<String> ssSources = new ArrayList<>(hSSConsensusProfileMap.keySet());
+ List<String> ssSources = new ArrayList<>(
+ hSSConsensusProfileMap.keySet());
secondaryStructureSources = new ArrayList<String>();
// Sort the secondary structure sources alphabetically
Collections.sort(ssSources);
-
+
// Initialize ssConsensus if it is null
if (ssConsensus == null)
{
getSSConsensus(ssSources);
}
-
+
// Iterate through each alignment annotation in the ssConsensus list
- for (AlignmentAnnotation aa : ssConsensus) {
+ for (AlignmentAnnotation aa : ssConsensus)
+ {
ProfilesI profile = null;
String ssSource = null;
-
- // Find the matching profile for the current annotation based on its description
- for(String source : ssSources) {
- if(aa.description.startsWith(source)) {
+
+ // Find the matching profile for the current annotation based on its
+ // description
+ for (String source : ssSources)
+ {
+ if (aa.description.startsWith(source))
+ {
profile = hSSConsensusProfileMap.get(source);
ssSource = source;
}
}
-
+
// If no matching profile is found, continue to the next annotation
- if(profile == null) {
+ if (profile == null)
+ {
continue;
}
- // Update the label and description of the annotation with the source/provider
- aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + ssSource + " " + getName();
- aa.description = ssSource + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL +" for " + getName();
-
+ // Update the label and description of the annotation with the
+ // source/provider
+ aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " "
+ + ssSource + " " + getName();
+ aa.description = ssSource
+ + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " for "
+ + getName();
+
// Get the width of the annotations array
int aWidth = (aa.annotations != null)
- ? (endRes < aa.annotations.length
- ? aa.annotations.length
+ ? (endRes < aa.annotations.length ? aa.annotations.length
: endRes + 1)
: endRes + 1;
- aa.annotations = new Annotation[aWidth];
-
+ aa.annotations = new Annotation[aWidth];
+
// Complete the secondary structure consensus
AAFrequency.completeSSConsensus(aa, profile, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo, nseq);
-
- //Add the provider to the list if the no of sequences
- //contributed to the secondary structure consensus is
- //more than 0.
- if(aa.getNoOfSequencesIncluded()>0 && !Constants.SS_ALL_PROVIDERS.equals(ssSource))
- {
+ ignoreGapsInConsensus, showSequenceLogo, nseq);
+
+ // Add the provider to the list if the no of sequences
+ // contributed to the secondary structure consensus is
+ // more than 0.
+ if (aa.getNoOfSequencesIncluded() > 0
+ && !Constants.SS_ALL_PROVIDERS.equals(ssSource))
+ {
// Remove "All" from the hidden types list{
secondaryStructureSources.add(ssSource);
}
consensus = aan;
}
}
-
+
public void setSSConsensusRow(AlignmentAnnotation aan)
{
ssConsensus = new ArrayList<AlignmentAnnotation>();
ssConsensus.add(aan);
}
- else {
+ else
+ {
boolean annotExists = ssConsensus.stream()
.anyMatch(ssa -> ssa.label.equals(aan.label));
- if(!annotExists) {
+ if (!annotExists)
+ {
ssConsensus.add(aan);
}
}
}
return consensus;
}
-
+
public List<AlignmentAnnotation> getSSConsensus(List<String> ssSources)
{
// TODO get or calculate and get consensus annotation row for this group
{
return null;
}
- if (ssConsensus == null && ssSources!=null)
+ if (ssConsensus == null && ssSources != null)
{
ssConsensus = new ArrayList<AlignmentAnnotation>();
-
- for(String ssSource : ssSources) {
- AlignmentAnnotation aa = new AlignmentAnnotation("", "", new Annotation[1], 0f,
- 100f, AlignmentAnnotation.BAR_GRAPH);
- // Setting the annotation visibility to true of the provider is "All"
+
+ for (String ssSource : ssSources)
+ {
+ AlignmentAnnotation aa = new AlignmentAnnotation("", "",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ // Setting the annotation visibility to true of the provider is "All"
// and false otherwise.
aa.visible = Constants.SS_ALL_PROVIDERS.equals(ssSource);
aa.hasText = true;
aa.autoCalculated = true;
aa.groupRef = this;
- aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + ssSource + " " + getName();
- aa.description = ssSource + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL +" for " + getName();
+ aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " "
+ + ssSource + " " + getName();
+ aa.description = ssSource
+ + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " for "
+ + getName();
ssConsensus.add(aa);
}
-
+
}
return ssConsensus;
}
}
this.showSequenceLogo = showSequenceLogo;
}
-
+
/**
*
* @param showConsHist
}
else
{
- PDBEntry ppe=getPdbEntry(pe);
- if (ppe==null) {
- Console.warn("Please report under JAL-4440: Unexpected null entry for PDBEntry for a structure (for structure "+fileName+")");
-
+ PDBEntry ppe = getPdbEntry(pe);
+ if (ppe == null)
+ {
+ Console.warn(
+ "Please report under JAL-4440: Unexpected null entry for PDBEntry for a structure (for structure "
+ + fileName + ")");
+
continue;
}
- if (ppe.getFile()==null)
+ if (ppe.getFile() == null)
{
- Console.warn("Please report under JAL-4440: Unexpected null entry for file that we just tried to load into Jmol: pdbEntry: "+ppe.toString()+"(for structure "+fileName+")");
+ Console.warn(
+ "Please report under JAL-4440: Unexpected null entry for file that we just tried to load into Jmol: pdbEntry: "
+ + ppe.toString() + "(for structure " + fileName
+ + ")");
continue;
}
File fl = new File(getPdbEntry(pe).getFile());
//// ***************************************************
//// TODO REFACTOR TREE I/O TO CONTROLLER/SEPARATE CLASS
//// ***************************************************
-
+
/**
* DOCUMENT ME!
*
return tp;
}
- public TreePanel showNewickTreeForAnnotation(NewickFile nf, String treeTitle,
- AlignmentView input, int w, int h, int x, int y)
+
+ public TreePanel showNewickTreeForAnnotation(NewickFile nf,
+ String treeTitle, AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
if (nf.getTree() != null)
{
- tp = TreePanel.newTreeForAnnotations(alignPanel, nf, treeTitle, input);
+ tp = TreePanel.newTreeForAnnotations(alignPanel, nf, treeTitle,
+ input);
// TODO - refactor layout code to one place for tree view methods
tp.setSize(w, h);
return tp;
}
-
public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
{
int x = 4, y = 5;
{
viewport.setShowStructureProvider(showStrucProvider.getState());
alignPanel.paintAlignment(false, false);
-
+
}
+
@Override
protected void updateShowSecondaryStructureMenu(JMenu showSS,
ButtonGroup ssButtonGroup)
.getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
viewStyle.setScaleProteinAsCdna(
Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
- viewStyle.setShowStructureProvider(Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false));
+ viewStyle.setShowStructureProvider(
+ Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false));
}
void init()
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
-
+
showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
{
ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
-
-
+
List<AlignCalcWorkerI> workers = ap.av.getCalcManager()
- .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
- if (!workers.isEmpty()) {
-
- ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0));
+ .getRegisteredWorkersOfClass(
+ SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty())
+ {
+
+ ap.alignFrame.getViewport().getCalcManager()
+ .startWorker(workers.remove(0));
}
}
{
msg.append(aa.sequenceRef.getName()).append(" : ");
}
-
+
if (aa.graphGroup == -1)
{
msg.append(aa.label);
- if(aa.getNoOfSequencesIncluded()>=0)
+ if (aa.getNoOfSequencesIncluded() >= 0)
{
msg.append(" (");
msg.append(MessageManager.getString("label.sequence_count"));
msg.append(")");
}
}
-
+
else if (anns != null)
{
boolean first = true;
// jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
// tooltips
String desc = aa.getDescription(true).trim();
- if(aa.getNoOfSequencesIncluded()>=0) {
+ if (aa.getNoOfSequencesIncluded() >= 0)
+ {
desc += " (" + MessageManager.getString("label.sequence_count")
- + aa.getNoOfSequencesIncluded()
- + ")";
+ + aa.getNoOfSequencesIncluded() + ")";
}
if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
{
vertBar = true;
}
}
-
- if(isShowStructureProvider && aa[i].hasIcons && Constants.SECONDARY_STRUCTURE_LABELS.keySet().contains(aa[i].label)) {
- String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa[i]);
- if(ssSource != null && ssSource.length()>0)
- label += " (" + ssSource + ")";
+
+ if (isShowStructureProvider && aa[i].hasIcons
+ && Constants.SECONDARY_STRUCTURE_LABELS.keySet()
+ .contains(aa[i].label))
+ {
+ String ssSource = AlignmentUtils
+ .extractSSSourceFromAnnotationDescription(aa[i]);
+ if (ssSource != null && ssSource.length() > 0)
+ label += " (" + ssSource + ")";
}
int labelWidth = fm.stringWidth(label) + 3;
public boolean isRepainting()
{
- if (renderPanel!=null && renderPanel.isVisible())
+ if (renderPanel != null && renderPanel.isVisible())
{
return renderPanel.repainting;
}
return false;
}
+
/**
* Outputs the Jmol viewer image as an image file, after prompting the user to
* choose a file and (for EPS) choice of Text or Lineart character rendering
{
while (!isRepainting())
{
- try {
+ try
+ {
Thread.sleep(2);
} catch (Exception q)
- {}
+ {
+ }
}
try
{
}
else
{
- repainting=true;
+ repainting = true;
synchronized (jmb)
{
jmb.jmolViewer.renderScreenImage(g, currentSize.width,
currentSize.height);
-
+
}
- repainting=false;
+ repainting = false;
}
}
- volatile boolean repainting=false;
+
+ volatile boolean repainting = false;
}
@Override
final JComboBox<String> comboBox = new JComboBox<>();
Object curSel = comboBox.getSelectedItem();
DefaultComboBoxModel<String> sourcesModel = new DefaultComboBoxModel<>();
-
+
List<String> ssSources = getApplicableSecondaryStructureSources();
-
- if(ssSources == null) {
+
+ if (ssSources == null)
+ {
return comboBox;
}
- ssSources.add(0, MessageManager.getString("option.ss_providers_all"));
+ ssSources.add(0, MessageManager.getString("option.ss_providers_all"));
boolean selectedIsPresent = false;
for (String source : ssSources)
*
* @param nucleotide
* @param forPca
- * @param ssPresent - include secondary structure similarity model
- * @param forPasimap - limit to ScoreMatrix based models - allows use of AlignSeq
+ * @param ssPresent
+ * - include secondary structure similarity model
+ * @param forPasimap
+ * - limit to ScoreMatrix based models - allows use of AlignSeq
* @return
*/
protected static List<ScoreModelI> getApplicableScoreModels(
ScoreModels scoreModels = ScoreModels.getInstance();
for (ScoreModelI sm : scoreModels.getModels())
{
- if ((!forPasimap || sm instanceof ScoreMatrix)
+ if ((!forPasimap || sm instanceof ScoreMatrix)
&& (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
|| sm.isSecondaryStructure() && ssPresent))
protected List<String> getApplicableSecondaryStructureSources()
{
- AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
-
- List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+ AlignmentAnnotation[] annotations = af.getViewport().getAlignment()
+ .getAlignmentAnnotation();
+
+ List<String> ssSources = AlignmentUtils
+ .extractSSSourceInAlignmentAnnotation(annotations);
return ssSources;
}
: modelNames.getSelectedItem().toString();
String ssSource = null;
-
- if (modelName.equals(secondaryStructureModelName)) {
+
+ if (modelName.equals(secondaryStructureModelName))
+ {
Object selectedItem = ssSourceDropdown.getSelectedItem();
- if (selectedItem != null) {
- ssSource = selectedItem.toString();
+ if (selectedItem != null)
+ {
+ ssSource = selectedItem.toString();
}
}
SimilarityParams params = getSimilarityParameters(doPCA);
params.setSecondaryStructureSource(ssSource);
-
+
if (doPCA)
{
openPcaPanel(modelName, params);
/**
* set font size of the textarea
+ *
* @param size
*/
public void setFont(Font font)
{
textarea.setFont(font);
}
-
+
/**
* DOCUMENT ME!
*/
{
}
}
-
+
/**
- * show menu for changing the font
- * @param e
- */
+ * show menu for changing the font
+ *
+ * @param e
+ */
@Override
public void fontSizeMenu_actionPerformed(ActionEvent e)
{
if (progressBars.get(Long.valueOf(id)) == null)
return null;
-
+
for (Component c : progressBars.get(Long.valueOf(id)).getComponents())
{
if (c.getClass() == JProgressBar.class)
- return (JProgressBar) c;
+ return (JProgressBar) c;
}
return null;
}
/**
* Creates a new FontChooser for a CutAndPasteTransfer
+ *
* @param cap
- */
+ */
public FontChooser(CutAndPasteTransfer cap)
{
oldFont = new Font("Monospaced", Font.PLAIN, 12);
if (!isCapFont())
{
smoothFont.setSelected(ap.av.antiAlias);
-
+
/*
* Enable 'scale protein as cDNA' in a SplitFrame view. The selection is
* stored in the ViewStyle of both dna and protein Viewport. Also enable
{
return cap != null;
}
+
/**
* DOCUMENT ME!
*/
setRotatableCanvas(new RotatableCanvas(alignPanel));
- if(params.getSecondaryStructureSource()!=null ) {
+ if (params.getSecondaryStructureSource() != null)
+ {
// Initialize and set subtitle text
- JLabel subtitleLabel = new JLabel(" Secondary Structure Provider : "
- + params.getSecondaryStructureSource(), SwingConstants.LEFT);
- this.getContentPane().add(subtitleLabel, BorderLayout.NORTH);
-
+ JLabel subtitleLabel = new JLabel(
+ " Secondary Structure Provider : "
+ + params.getSecondaryStructureSource(),
+ SwingConstants.LEFT);
+ this.getContentPane().add(subtitleLabel, BorderLayout.NORTH);
+
}
this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
*/
public PaSiMapPanel(AlignmentPanel alignPanel, String modelName)
{
- super(8); // dim = 8
+ super(8); // dim = 8
this.av = alignPanel.av;
this.ap = alignPanel;
boolean nucleotide = av.getAlignment().isNucleotide();
- //progressBar = new ProgressBar(statusPanel, statusBar);
+ // progressBar = new ProgressBar(statusPanel, statusBar);
addInternalFrameListener(new InternalFrameAdapter()
{
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
- setPasimapModel(
- new PaSiMapModel(av, seqs, nucleotide, scoreModel));
+ setPasimapModel(new PaSiMapModel(av, seqs, nucleotide, scoreModel));
PaintRefresher.Register(this, av.getSequenceSetId());
setRotatableCanvas(new RotatableCanvas(alignPanel));
}
/**
- * Ensure references to potentially very large objects (the PaSiMap matrices) are
- * nulled when the frame is closed
+ * Ensure references to potentially very large objects (the PaSiMap matrices)
+ * are nulled when the frame is closed
*/
protected void close_actionPerformed()
{
progressBar.setProgressBar(message, progId);
try
{
- SequenceGroup selGroup=av.getSelectionGroup();
-
- if (selGroup==null)
+ SequenceGroup selGroup = av.getSelectionGroup();
+
+ if (selGroup == null)
{
selGroup = new SequenceGroup(av.getAlignment().getSequences());
selGroup.setStartRes(0);
- selGroup.setEndRes(av.getAlignment().getWidth()-1);
+ selGroup.setEndRes(av.getAlignment().getWidth() - 1);
}
-
- if (selGroup.getSize()>MAX_PASIMAP_SEQ)
+
+ if (selGroup.getSize() > MAX_PASIMAP_SEQ)
{
- int start = selGroup.getStartRes(),end=selGroup.getEndRes();
- selGroup = new SequenceGroup(selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
- selGroup.setStartRes(start);
- selGroup.setEndRes(end);
- Console.warn("Truncated input sequences for PASIMAP analysis to "+MAX_PASIMAP_SEQ);
+ int start = selGroup.getStartRes(), end = selGroup.getEndRes();
+ selGroup = new SequenceGroup(
+ selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
+ selGroup.setStartRes(start);
+ selGroup.setEndRes(end);
+ Console.warn("Truncated input sequences for PASIMAP analysis to "
+ + MAX_PASIMAP_SEQ);
}
-
+
PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true,
GAP_OPEN_COST, GAP_EXTEND_COST, false, null);
pap.setDiscardAlignments(true);
pap.setQuiet(true);
-
+
System.out.println(pap != null);
setPairwiseAlignPanel(pap);
getPasimapModel().calculate(pap);
repaint();
if (getParent() == null)
{
- Desktop.addInternalFrame(
- this, MessageManager.formatMessage("label.calc_title",
- "PaSiMap", ap.alignFrame.getTitle()),
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PaSiMap",
+ ap.alignFrame.getTitle()),
475, 450);
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
}
/**
- * Updates the PaSiMap display after a change of component to use for x, y or z
- * axis
+ * Updates the PaSiMap display after a change of component to use for x, y or
+ * z axis
*/
@Override
protected void doDimensionChange()
}
/**
- * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for
- * the given axis (X/Y/Z)
+ * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...)
+ * for the given axis (X/Y/Z)
*
* @param index
* @param axis
}
/**
- * If available, shows the data which formed the inputs for the PaSiMap as a new
- * alignment
+ * If available, shows the data which formed the inputs for the PaSiMap as a
+ * new alignment
*/
@Override
public void originalSeqData_actionPerformed()
}
}
- public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
+ public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
{
int width = getRotatableCanvas().getWidth();
int height = getRotatableCanvas().getHeight();
{
cap.setText(getPasimapModel().getAlignmentOutput());
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
+ "label.pairwise_alignment_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting pairwise alignments", oom);
public void updateProgressBar(int lengthOfTask, int progress)
{
JProgressBar pBar = progressBar.getProgressBar(progId);
- if (pBar==null)
+ if (pBar == null)
{
return;
}
}
updateProgressBar(progress);
}
+
public void updateProgressBar(int progress)
{
JProgressBar pBar = progressBar.getProgressBar(progId);
-
- if (pBar==null)
+
+ if (pBar == null)
{
return;
}
-
+
pBar.setValue(progress);
pBar.repaint();
}
/**
- * adds a listener for a pairwise alignment panel's progress
- * TODO: generalise for anything that can report progress ?
+ * adds a listener for a pairwise alignment panel's progress TODO: generalise
+ * for anything that can report progress ?
+ *
* @param pap
*/
public void setPairwiseAlignPanel(PairwiseAlignPanel pap)
}
/**
- * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or
- * Z axis of the display
+ * Answers the selected checkbox item index for PaSiMap dimension for the X, Y
+ * or Z axis of the display
*
* @param axis
* @return
private float[][] scores;
- private float[][] alignmentScores; // scores used by PaSiMap
+ private float[][] alignmentScores; // scores used by PaSiMap
private int GAP_OPEN_COST;
private String alignmentOutput;
private boolean quiet;
-
+
private boolean discardAlignments;
private boolean endGaps;
private int total;
private int progress;
-
+
private SequenceGroup selection;
+
/**
* input sequences
*/
- private SequenceI[] seqs=null;
+ private SequenceI[] seqs = null;
private ScoreMatrix scoreMatrix;
*
* @param viewport
* contains selected sequences to align
- * @param endGaps ~ toggle gaps and the beginning and end of sequences
+ * @param endGaps
+ * ~ toggle gaps and the beginning and end of sequences
*/
public PairwiseAlignPanel(AlignmentViewport viewport)
{
- this(viewport, null, false, 120, 20, true, null); // default penalties used in AlignSeq
+ this(viewport, null, false, 120, 20, true, null); // default penalties used
+ // in AlignSeq
}
+
public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)
{
- this(viewport, null, false, 120, 20, true,params); // default penalties used in AlignSeq
+ this(viewport, null, false, 120, 20, true, params); // default penalties
+ // used in AlignSeq
}
- public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps,
+ int gapOpenCost, int gapExtendCost)
{
this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null);
}
/**
- * Create a new pairwise alignpanel with specified parameters and score model, and optionally start the calculation
+ * Create a new pairwise alignpanel with specified parameters and score model,
+ * and optionally start the calculation
+ *
* @param viewport
* @param selection
* @param endGaps
* @param run
* @param scoreMatrix
*/
- public PairwiseAlignPanel(AlignmentViewport viewport, SequenceGroup selection, boolean endGaps,
- int gapOpenCost, int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
+ public PairwiseAlignPanel(AlignmentViewport viewport,
+ SequenceGroup selection, boolean endGaps, int gapOpenCost,
+ int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
{
super();
this.av = viewport;
this.selection = selection;
this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
this.scoreMatrix = scoreMatrix;
- if (run) {
+ if (run)
+ {
calculate();
}
}
-
+
public void calculate()
{
calculate(scoreMatrix);
}
- public void calculate (ScoreMatrix sm)
+
+ public void calculate(ScoreMatrix sm)
{
StringBuilder sb = new StringBuilder(1024);
sequences = new Vector<SequenceI>();
String[] seqStrings;
- seqs=null;
+ seqs = null;
if (selection != null)
{
seqs = av.getAlignment().getSequencesArray();
}
}
-
+
String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
float[][] alignmentScores = new float[seqs.length][seqs.length];
double totscore = 0D;
int count = seqs.length;
-
+
boolean first = true;
progress = 0;
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
- if (sm != null) {
- as.setScoreMatrix(sm);
- }
+ if (sm != null)
+ {
+ as.setScoreMatrix(sm);
+ }
- if (as.s1str.length() == 0 || as.s2str.length() == 0)
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
continue;
}
sb.append(DASHES);
}
first = false;
- if (!discardAlignments) {
+ if (!discardAlignments)
+ {
as.printAlignment(System.out);
}
scores[i][j] = as.getMaxScore() / as.getASeq1().length;
this.scores = scores;
this.alignmentScores = alignmentScores;
- if (count > 2 && !quiet)
+ if (count > 2 && !quiet)
{
printScoreMatrix(seqs, scores, totscore);
}
{
return progress;
}
+
public SequenceI[] getInputSequences()
{
return seqs;
}
+
/**
- * Set to true to suppress output of progress to Console.stdout or GUI
- * @param quiet
+ * Set to true to suppress output of progress to Console.stdout or GUI
+ *
+ * @param quiet
*/
public void setQuiet(boolean quiet)
{
- this.quiet=quiet;
+ this.quiet = quiet;
}
+
/**
* set this if you are only interested in final alignment scores
+ *
* @param discard
*/
public void setDiscardAlignments(boolean discard)
{
- discardAlignments=discard;
+ discardAlignments = discard;
}
}
JMenuItem textColour = new JMenuItem();
- JMenu editGroupMenu = new JMenu();
+ JMenu editGroupMenu = new JMenu();
- JMenu groupShowAutoCalculatedAnnotations = new JMenu();
+ JMenu groupShowAutoCalculatedAnnotations = new JMenu();
JMenu groupHideAutoCalculatedAnnotations = new JMenu();
final List<SequenceI> selectedGroup = (alignPanel.av
.getSelectionGroup() == null
? Collections.<SequenceI> emptyList()
- : alignPanel.av.getSelectionGroup().getSequences());
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
selectedGroup);
-
- //If a sequence group is selected, build show/hide auto calculated annotations menu
+
+ // If a sequence group is selected, build show/hide auto calculated
+ // annotations menu
SequenceGroup selectedSequenceGroup = alignPanel.av.getSelectionGroup();
- if(selectedSequenceGroup != null) {
- buildAutoCalculatedAnnotationsMenu(groupShowAutoCalculatedAnnotations,
+ if (selectedSequenceGroup != null)
+ {
+ buildAutoCalculatedAnnotationsMenu(groupShowAutoCalculatedAnnotations,
groupHideAutoCalculatedAnnotations, selectedSequenceGroup);
}
ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
conservationMenuItem.setEnabled(!sg.isNucleotide());
-
+
byConsensusSecondaryStructureMenuItem.setEnabled(!sg.isNucleotide());
if (sg.cs != null)
{
abovePIDColour.setSelected(true);
}
- if(sg.cs.isConsensusSecondaryStructureColouring())
+ if (sg.cs.isConsensusSecondaryStructureColouring())
{
byConsensusSecondaryStructureMenuItem.setSelected(true);
}
unGroupMenuItem.setVisible(false);
editGroupMenu
.setText(MessageManager.getString("action.edit_new_group"));
-
- // Hide show/hide auto calculated annotations menus for group if a sequence
- // group is not defined.
+
+ // Hide show/hide auto calculated annotations menus for group if a
+ // sequence
+ // group is not defined.
groupShowAutoCalculatedAnnotations.setVisible(false);
groupHideAutoCalculatedAnnotations.setVisible(false);
}
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
editGroupMenu.setText(MessageManager.getString("action.edit_group"));
-
- // Show show/hide auto calculated annotations menus for group if a sequence
- // group is defined and showGroupSSConsensus is true. Hide the menus otherwise.
- if(alignPanel.av.isShowGroupSSConsensus()) {
+
+ // Show show/hide auto calculated annotations menus for group if a
+ // sequence
+ // group is defined and showGroupSSConsensus is true. Hide the menus
+ // otherwise.
+ if (alignPanel.av.isShowGroupSSConsensus())
+ {
groupShowAutoCalculatedAnnotations.setVisible(true);
groupHideAutoCalculatedAnnotations.setVisible(true);
}
- else {
+ else
+ {
groupShowAutoCalculatedAnnotations.setVisible(false);
groupHideAutoCalculatedAnnotations.setVisible(false);
}
// grey out 'hide annotations' if none are shown
hideMenu.setEnabled(!shownTypes.isEmpty());
}
-
+
/**
* Builds the menu for showing and hiding auto calculated annotations for a
* selected sequence group. It clears existing menu items and adds menu items
AlignmentAnnotationUtils.asList(annotations),
selectedSequenceGroup);
- // Add code if additional auto calculated annotation types (like residue consensus,
+ // Add code if additional auto calculated annotation types (like residue
+ // consensus,
// conservation, etc.) are needed for a selected group
// Add currently hidden types to the show menu
groupShowAutoCalculatedAnnotations.setEnabled(!hiddenTypes.isEmpty());
groupHideAutoCalculatedAnnotations.setEnabled(!shownTypes.isEmpty());
}
-
-
+
/**
* Adds a menu item to the provided menu for showing or hiding a specific type
* of auto calculated annotation
* @param type
* The type of annotation to show or hide.
* @param allTypes
- * Indicates if the action should apply to all annotation types.
- * True if user selects "All".
+ * Indicates if the action should apply to all annotation types. True
+ * if user selects "All".
* @param actionIsShow
* Indicates if the item is for showing (true) or hiding (false) the
* annotation type.
showOrHideAutoCalculatedAnnotationsMenu.add(item);
}
-
-
/**
* Returns a list of sequences - either the current selection group (if there
* is one), else the specified single sequence.
.setText(MessageManager.getString("label.show_annotations"));
groupHideAnnotationsMenu
.setText(MessageManager.getString("label.hide_annotations"));
- groupShowAutoCalculatedAnnotations
- .setText(MessageManager.getString("label.group_show_auto_calculated_annotations"));
- groupHideAutoCalculatedAnnotations
- .setText(MessageManager.getString("label.group_hide_auto_calculated_annotations"));
+ groupShowAutoCalculatedAnnotations.setText(MessageManager
+ .getString("label.group_show_auto_calculated_annotations"));
+ groupHideAutoCalculatedAnnotations.setText(MessageManager
+ .getString("label.group_hide_auto_calculated_annotations"));
JMenuItem sequenceFeature = new JMenuItem(
MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
conservationMenuItem.isSelected());
}
});
-
- byConsensusSecondaryStructureMenuItem.setText(
- MessageManager.getString("action.by_secondary_structure_conservation"));
- byConsensusSecondaryStructureMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- colourByConsensusSecondaryStructureMenuItem_actionPerformed(
- byConsensusSecondaryStructureMenuItem.isSelected());
- }
- });
+
+ byConsensusSecondaryStructureMenuItem.setText(MessageManager
+ .getString("action.by_secondary_structure_conservation"));
+ byConsensusSecondaryStructureMenuItem
+ .addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourByConsensusSecondaryStructureMenuItem_actionPerformed(
+ byConsensusSecondaryStructureMenuItem.isSelected());
+ }
+ });
annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
modifyConservation_actionPerformed();
}
});
-
- modifyConsensusSecondaryStructureThreshold.setText(MessageManager
- .getString("label.modify_secondary_structure_conservation_threshold"));
- modifyConsensusSecondaryStructureThreshold.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConsensusSecondaryStructureThreshold_actionPerformed();
- }
- });
+
+ modifyConsensusSecondaryStructureThreshold
+ .setText(MessageManager.getString(
+ "label.modify_secondary_structure_conservation_threshold"));
+ modifyConsensusSecondaryStructureThreshold
+ .addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConsensusSecondaryStructureThreshold_actionPerformed();
+ }
+ });
}
/**
SliderPanel.showConservationSlider();
}
}
-
+
protected void modifyConsensusSecondaryStructureThreshold_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg.cs != null)
{
- SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.cs, sg.getName());
+ SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.cs,
+ sg.getName());
SliderPanel.showConsensusSecondaryStructureSlider();
}
}
-
protected void modifyPID_actionPerformed()
{
{
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
-
- if(AlignmentUtils.isSSAnnotationPresent(candidates)) {
-
+
+ if (AlignmentUtils.isSSAnnotationPresent(candidates))
+ {
+
restartSSConsensusWorker();
ap.validateAnnotationDimensions(true);
ap.fontChanged();
ap.av.alignmentChanged(ap);
ap.adjustAnnotationHeight();
restartSSConsensusWorker();
- //ap.alignFrame.getViewport().getCalcManager().restartWorkers();
+ // ap.alignFrame.getViewport().getCalcManager().restartWorkers();
}
-
+
}
-
-
- private void restartSSConsensusWorker() {
-
- List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport().getCalcManager()
- .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
- if (!workers.isEmpty()) {
-
- ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0));
-
- }
-
+
+ private void restartSSConsensusWorker()
+ {
+
+ List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport()
+ .getCalcManager().getRegisteredWorkersOfClass(
+ SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty())
+ {
+
+ ap.alignFrame.getViewport().getCalcManager()
+ .startWorker(workers.remove(0));
+
+ }
+
}
-
-
protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
refresh();
}
-
- public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(boolean selected)
+
+ public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(
+ boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
if (selected)
{
-
+
sg.cs.setConsensusSecondaryStructureColouring(selected);
- SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.getGroupColourScheme(),
- sg.getName());
+ SliderPanel.setConsensusSecondaryStructureSlider(ap,
+ sg.getGroupColourScheme(), sg.getName());
SliderPanel.showConsensusSecondaryStructureSlider();
}
else
public JProgressBar getProgressBar(long id)
{
Container progBar = progressBars.get(id);
- if (progBar==null || progBar.getComponentCount()==0)
+ if (progBar == null || progBar.getComponentCount() == 0)
{
return null;
}
private Point[] axisEndPoints;
// fields for 'select rectangle' (JAL-1124)
- int rectx1;
- int recty1;
- int rectx2;
- int recty2;
+ int rectx1;
+
+ int recty1;
+
+ int rectx2;
+
+ int recty2;
AlignmentViewport av;
}
}
// //Now the rectangle
- if (rectx2 != -1 && recty2 != -1) {
- g.setColor(Color.white);
-
- g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
- }
+ if (rectx2 != -1 && recty2 != -1)
+ {
+ g.setColor(Color.white);
+
+ g.drawRect(rectx1, recty1, rectx2 - rectx1, recty2 - recty1);
+ }
}
/**
mouseX = x;
mouseY = y;
- rectx1 = x;
- recty1 = y;
- rectx2 = -1;
- recty2 = -1;
+ rectx1 = x;
+ recty1 = y;
+ rectx2 = -1;
+ recty2 = -1;
SequenceI found = findSequenceAtPoint(x, y);
// Check if this is a rectangle drawing drag
if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
{
- rectx2 = evt.getX();
- recty2 = evt.getY();
- if ((rectx2 != -1) && (recty2 != -1))
- {
- rectSelect(rectx1, recty1, rectx2, recty2);
- }
+ rectx2 = evt.getX();
+ recty2 = evt.getY();
+ if ((rectx2 != -1) && (recty2 != -1))
+ {
+ rectSelect(rectx1, recty1, rectx2, recty2);
+ }
}
else
{
mouseY = yPos;
// findWidths();
}
- repaint();
+ repaint();
}
@Override
{
SequencePoint sp = sequencePoints.get(i);
int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor())
- * (getWidth() / 3.15)
- + (getWidth() / 2.0));
+ * (getWidth() / 3.15) + (getWidth() / 2.0));
float pre1 = ((sp.coord.x - centre[0]) * getScaleFactor());
int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor())
- * (getHeight() / 1.70)
- + (getHeight() / 2.0));
+ * (getHeight() / 1.70) + (getHeight() / 2.0));
float pre2 = ((sp.coord.y - centre[1]) * getScaleFactor());
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
}
if (stretchGroup.cs.isConsensusSecondaryStructureColouring())
{
- SliderPanel.setConsensusSecondaryStructureSlider(ap, groupColourScheme, name);
+ SliderPanel.setConsensusSecondaryStructureSlider(ap,
+ groupColourScheme, name);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
private static final String BACKGROUND = "Background";
static JInternalFrame conservationSlider;
-
+
static JInternalFrame consensusSecondaryStructureSlider;
static JInternalFrame PIDSlider;
AlignmentPanel ap;
boolean forConservation = true;
-
+
boolean forConsensusSecondaryStructure = false;
ResidueShaderI cs;
{
return (SliderPanel) PIDSlider.getContentPane();
}
- if (consensusSecondaryStructureSlider != null && consensusSecondaryStructureSlider.isVisible())
+ if (consensusSecondaryStructureSlider != null
+ && consensusSecondaryStructureSlider.isVisible())
{
- return (SliderPanel) consensusSecondaryStructureSlider.getContentPane();
+ return (SliderPanel) consensusSecondaryStructureSlider
+ .getContentPane();
}
return null;
}
* DOCUMENT ME!
*/
public SliderPanel(final AlignmentPanel ap, int value,
- boolean forConserve, boolean forConsensusSS, ResidueShaderI scheme)
+ boolean forConserve, boolean forConsensusSS,
+ ResidueShaderI scheme)
{
this.ap = ap;
this.cs = scheme;
forConservation = forConserve;
forConsensusSecondaryStructure = forConsensusSS;
-
+
undoButton.setVisible(false);
applyButton.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
}
- if(forConsensusSS) {
+ if (forConsensusSS)
+ {
label.setText(MessageManager.getString(
"label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
if (conservationSlider == null)
{
- sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, false, rs);
+ sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true,
+ false, rs);
conservationSlider = new JInternalFrame();
conservationSlider.setFrameIcon(null);
conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
}
-
+
public static int setConsensusSecondaryStructureSlider(AlignmentPanel ap,
ResidueShaderI rs, String source)
{
if (consensusSecondaryStructureSlider == null)
{
- sliderPanel = new SliderPanel(ap, rs.getConsensusSecondaryStructureThreshold(), false, true, rs);
+ sliderPanel = new SliderPanel(ap,
+ rs.getConsensusSecondaryStructureThreshold(), false, true,
+ rs);
consensusSecondaryStructureSlider = new JInternalFrame();
consensusSecondaryStructureSlider.setFrameIcon(null);
consensusSecondaryStructureSlider.setContentPane(sliderPanel);
- consensusSecondaryStructureSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ consensusSecondaryStructureSlider
+ .setLayer(JLayeredPane.PALETTE_LAYER);
}
else
{
- sliderPanel = (SliderPanel) consensusSecondaryStructureSlider.getContentPane();
- sliderPanel.valueField
- .setText(String.valueOf(rs.getConsensusSecondaryStructureThreshold()));
+ sliderPanel = (SliderPanel) consensusSecondaryStructureSlider
+ .getContentPane();
+ sliderPanel.valueField.setText(
+ String.valueOf(rs.getConsensusSecondaryStructureThreshold()));
sliderPanel.cs = rs;
sliderPanel.ap = ap;
- sliderPanel.slider.setValue(rs.getConsensusSecondaryStructureThreshold());
+ sliderPanel.slider
+ .setValue(rs.getConsensusSecondaryStructureThreshold());
}
consensusSecondaryStructureSlider.setTitle(MessageManager.formatMessage(
return sliderPanel.getValue();
}
-
-
+
public static void hideConsensusSecondaryStructureSlider()
{
if (consensusSecondaryStructureSlider != null)
}
}
}
-
-
+
public static void showConsensusSecondaryStructureSlider()
{
hidePIDSlider();
if (!consensusSecondaryStructureSlider.isVisible())
{
Desktop.addInternalFrame(consensusSecondaryStructureSlider,
- consensusSecondaryStructureSlider.getTitle(), true, FRAME_WIDTH,
- FRAME_HEIGHT, false, true);
- consensusSecondaryStructureSlider.addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent e)
- {
- consensusSecondaryStructureSlider = null;
- }
- });
- consensusSecondaryStructureSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ consensusSecondaryStructureSlider.getTitle(), true,
+ FRAME_WIDTH, FRAME_HEIGHT, false, true);
+ consensusSecondaryStructureSlider
+ .addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ consensusSecondaryStructureSlider = null;
+ }
+ });
+ consensusSecondaryStructureSlider
+ .setLayer(JLayeredPane.PALETTE_LAYER);
}
}
{
scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
}
- if(forConsensusSecondaryStructure)
+ if (forConsensusSecondaryStructure)
{
scheme.setConsensusSecondaryStructureColouring(true);
scheme.setConsensusSecondaryStructureThreshold(percent);
{
return getValue(PIDSlider);
}
-
+
public static int getConsensusSecondaryStructureSliderValue()
{
return getValue(consensusSecondaryStructureSlider);
{
title = PIDSlider.getTitle();
}
- else if(consensusSecondaryStructureSlider != null)
+ else if (consensusSecondaryStructureSlider != null)
{
title = consensusSecondaryStructureSlider.getTitle();
}
String pdbFilename = selectedPdbFileName;
// TODO - tidy up this ugly hack so we call launchStructureViewer too
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
- selectedSequence, true, pdbFilename, tft, paeFilename,false,
- true,false,getTargetedStructureViewer(ssm).getViewerType());
+ selectedSequence, true, pdbFilename, tft, paeFilename,
+ false, true, false,
+ getTargetedStructureViewer(ssm).getViewerType());
}
SwingUtilities.invokeLater(new Runnable()
{
* @param forceHeadless
* @param showRefAnnotations
* @param doXferSettings
- * @param viewerType - when not null means the viewer will be opened, providing forceHeadless/headless is not true
+ * @param viewerType
+ * - when not null means the viewer will be opened, providing
+ * forceHeadless/headless is not true
* @return
*/
public static StructureViewer openStructureFileForSequence(
ssm = ap.getStructureSelectionManager();
StructureSelectionManager.doConfigureStructurePrefs(ssm);
}
-
+
PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
tft, paeFilename, doXferSettings);
sc.mainFrame.dispose();
- // TODO should honor preferences - only show reference annotation that is requested - JAL-4415 JAL-3124
+ // TODO should honor preferences - only show reference annotation that is
+ // requested - JAL-4415 JAL-3124
if (showRefAnnotations)
{
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
has_placeholders = true;
}
- if (longestName.length() < lf.getDisplayName()
- .length())
+ if (longestName.length() < lf.getDisplayName().length())
{
- longestName = TreeCanvas.PLACEHOLDER
- + lf.getDisplayName();
+ longestName = TreeCanvas.PLACEHOLDER + lf.getDisplayName();
}
if (tp.isColumnWise() && cm != null)
{
}
if (node.hasLabel())
{
- nodeLabel = node.getLabel()+" "+nodeLabel;
+ nodeLabel = node.getLabel() + " " + nodeLabel;
}
if (!nodeLabel.equals(""))
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
- gatherLabelsTo(groups.get(i),l);
+ gatherLabelsTo(groups.get(i), l);
if (!tp.isColumnWise())
{
- createSeqGroupFor(aps, l, col);
+ createSeqGroupFor(aps, l, col);
}
else
{
private void gatherLabelsTo(BinaryNode binaryNode, Vector<BinaryNode> l)
{
LinkedHashSet<String> labelsForNode = new LinkedHashSet<String>();
- for (BinaryNode leaf:l)
+ for (BinaryNode leaf : l)
{
if (leaf.hasLabel())
{
}
}
StringBuilder sb = new StringBuilder();
- boolean first=true;
- for (String label:labelsForNode)
+ boolean first = true;
+ for (String label : labelsForNode)
{
- if (!first) {
+ if (!first)
+ {
sb.append(" | ");
}
- first=false;
+ first = false;
sb.append(label);
}
binaryNode.setLabel(sb.toString());
c.verdict(false, viewport.getConsPercGaps());
sg.cs.setConservation(c);
}
- if(viewport.getResidueShading().isConsensusSecondaryStructureColouring())
+ if (viewport.getResidueShading()
+ .isConsensusSecondaryStructureColouring())
{
sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold(
viewport.getResidueShading().getThreshold());
- sg.getGroupColourScheme().setConsensusSecondaryStructureColouring(true);
+ sg.getGroupColourScheme()
+ .setConsensusSecondaryStructureColouring(true);
}
}
// indicate that associated structure views will need an update
TreeModel tree;
private AlignViewport av;
-
// New JLabel for subtitle
private JLabel subtitleLabel;
public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
String theTitle, AlignmentView inputData)
{
- this(alignPanel, newtree, theTitle, inputData, null,null);
+ this(alignPanel, newtree, theTitle, inputData, null, null);
}
/**
boolean forAnnotation = false;
public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
- String theTitle, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations, String subTitle)
+ String theTitle, AlignmentView inputData,
+ AlignmentAnnotation[] leafAnnotations, String subTitle)
{
super();
- this.forAnnotation=leafAnnotations!=null && leafAnnotations.length>0;
+ this.forAnnotation = leafAnnotations != null
+ && leafAnnotations.length > 0;
this.setFrameIcon(null);
this.treeTitle = theTitle;
initTreePanel(alignPanel, null, null, newtree, inputData, null);
}
void initTreePanel(AlignmentPanel ap, String type, String modelName,
- NewickFile newTree, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations)
+ NewickFile newTree, AlignmentView inputData,
+ AlignmentAnnotation[] leafAnnotations)
{
av = ap.av;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
-
+
if (similarityParams != null
&& similarityParams.getSecondaryStructureSource() != null)
{
addSubtitlePanel(" Secondary Structure Provider : "
+ similarityParams.getSecondaryStructureSource());
}
- if (leafAnnotations!=null)
+ if (leafAnnotations != null)
{
- forAnnotation=true;
+ forAnnotation = true;
}
if (columnWise)
{
private AlignmentView odata = null;
private AlignmentAnnotation[] leafAnnotations;
- public TreeLoader(NewickFile newickFile, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations)
+
+ public TreeLoader(NewickFile newickFile, AlignmentView inputData,
+ AlignmentAnnotation[] leafAnnotations)
{
this.newtree = newickFile;
this.odata = inputData;
this.leafAnnotations = leafAnnotations;
-
+
if (newickFile != null)
{
// Must be outside run(), as Jalview2XML tries to
NewickFile nf, String treeTitle2, AlignmentView input)
{
// TODO - recover subpanel name
- TreePanel tp = new TreePanel(alignPanel, nf, treeTitle2, input, null, "Annotation Tree");
+ TreePanel tp = new TreePanel(alignPanel, nf, treeTitle2, input, null,
+ "Annotation Tree");
return tp;
}
}
String modelPage = humanUrl < 1 ? null
: (String) restable.getValueAt(row, humanUrl);
- String modelCategory = idx_mcat < 1 ? null :(String) restable.getValueAt(row,idx_mcat);
-
+ String modelCategory = idx_mcat < 1 ? null
+ : (String) restable.getValueAt(row, idx_mcat);
+
String strucFormat = restable.getValueAt(row, modelformat).toString();
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
sg.cs.setThreshold(Integer.parseInt(value), true);
}
- else if(key.equalsIgnoreCase("secondaryStructureConservationThreshold"))
+ else if (key
+ .equalsIgnoreCase("secondaryStructureConservationThreshold"))
{
- sg.cs.setConsensusSecondaryStructureThreshold(Integer.parseInt(value));
+ sg.cs.setConsensusSecondaryStructureThreshold(
+ Integer.parseInt(value));
sg.cs.setConsensusSecondaryStructureColouring(true);
-
+
}
else if (key.equalsIgnoreCase("consThreshold"))
{
protected JCheckBoxMenuItem abovePIDThreshold;
- protected JMenuItem modifyPID;
+ protected JMenuItem modifyPID;
protected JCheckBoxMenuItem byConsensusSecondaryStructureMenuItem;
-
+
protected JMenuItem modifyConsensusSecondaryStructureThreshold;
protected JRadioButtonMenuItem annotationColour;
protected JMenuItem gatherViews = new JMenuItem();
protected JMenuItem expandViews = new JMenuItem();
-
- protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showGroupSSConsensus = new JCheckBoxMenuItem();
-
+
protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
});
showStrucProvider = new JCheckBoxMenuItem(
MessageManager.getString("label.show_structure_provider"));
- showStrucProvider.addActionListener(new ActionListener() {
+ showStrucProvider.addActionListener(new ActionListener()
+ {
@Override
public void actionPerformed(ActionEvent e)
{
showStructureProvider_actionPerformed(e);
}
-
+
});
colourTextMenuItem = new JCheckBoxMenuItem(
MessageManager.getString("label.colour_text"));
});
- showSSConsensus
- .setText(MessageManager.getString("label.show_secondary_structure_consensus"));
+ showSSConsensus.setText(MessageManager
+ .getString("label.show_secondary_structure_consensus"));
showSSConsensus.addActionListener(new ActionListener()
{
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- showSSConsensus_actionPerformed(e);
- }
-
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showSSConsensus_actionPerformed(e);
+ }
+
});
-
+
showGroupSSConsensus
.setText(MessageManager.getString("label.group_ss_consensus"));
showGroupSSConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupSSConsensus_actionPerformed(e);
}
-
+
});
showGroupConsensus
showConsensusHistogram_actionPerformed(e);
}
- });
+ });
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
copyHighlighted.addActionListener(al);
- ButtonGroup ssButtonGroup = new ButtonGroup();
+ ButtonGroup ssButtonGroup = new ButtonGroup();
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
MessageManager.getString("label.autocalculated_annotation"));
JMenu showSS = new JMenu(
- MessageManager.getString("label.show_secondary_structure"));
-
- JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem(MessageManager.getString("option.ss_providers_all"));
- radioButtonAllSS.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- showOrHideSecondaryStructureForSource(MessageManager.getString("option.ss_providers_all"), true);
- // Select all checkboxes if "All" is selected
- Component[] components = showSS.getMenuComponents();
- for (Component component : components) {
- if (component instanceof JCheckBoxMenuItem) {
- ((JCheckBoxMenuItem) component).setSelected(true);
- }
+ MessageManager.getString("label.show_secondary_structure"));
+
+ JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem(
+ MessageManager.getString("option.ss_providers_all"));
+ radioButtonAllSS.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showOrHideSecondaryStructureForSource(
+ MessageManager.getString("option.ss_providers_all"), true);
+ // Select all checkboxes if "All" is selected
+ Component[] components = showSS.getMenuComponents();
+ for (Component component : components)
+ {
+ if (component instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) component).setSelected(true);
}
+ }
}
});
ssButtonGroup.add(radioButtonAllSS);
showSS.add(radioButtonAllSS);
-
- JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem(MessageManager.getString("option.ss_providers_none"));
- radioButtonNoneSS.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- showOrHideSecondaryStructureForSource(MessageManager.getString("option.ss_providers_none"), false);
- // Remove selection of all checkboxes if "None" is selected
- Component[] components = showSS.getMenuComponents();
- for (Component component : components) {
- if (component instanceof JCheckBoxMenuItem) {
- ((JCheckBoxMenuItem) component).setSelected(false);
- }
+
+ JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem(
+ MessageManager.getString("option.ss_providers_none"));
+ radioButtonNoneSS.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showOrHideSecondaryStructureForSource(
+ MessageManager.getString("option.ss_providers_none"),
+ false);
+ // Remove selection of all checkboxes if "None" is selected
+ Component[] components = showSS.getMenuComponents();
+ for (Component component : components)
+ {
+ if (component instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) component).setSelected(false);
}
+ }
}
});
ssButtonGroup.add(radioButtonNoneSS);
showSS.add(radioButtonNoneSS);
showSS.addSeparator();
-
- annotationsMenu.addMouseListener(new MouseAdapter() {
-
+
+ annotationsMenu.addMouseListener(new MouseAdapter()
+ {
+
@Override
- public void mouseEntered(MouseEvent e) {
+ public void mouseEntered(MouseEvent e)
+ {
+
+ updateShowSecondaryStructureMenu(showSS, ssButtonGroup); // Update radio
+ // buttons
+ // every time
+ // the menu is
+ // clicked
- updateShowSecondaryStructureMenu(showSS, ssButtonGroup); // Update radio buttons every time the menu is clicked
-
}
});
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
autoAnnMenu.add(normaliseSequenceLogo);
- //autoAnnMenu.add(showSSConsensus);
+ // autoAnnMenu.add(showSSConsensus);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
protected void showStructureProvider_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showSSConsensus_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void createPNG_actionPerformed(ActionEvent object)
conservationMenuItem.isSelected());
}
});
-
byConsensusSecondaryStructureMenuItem = new JCheckBoxMenuItem(
- MessageManager.getString("action.by_secondary_structure_conservation"));
- byConsensusSecondaryStructureMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- colourByConsensusSecondaryStructureMenuItem_actionPerformed(
- byConsensusSecondaryStructureMenuItem.isSelected());
- }
- });
+ MessageManager.getString(
+ "action.by_secondary_structure_conservation"));
+ byConsensusSecondaryStructureMenuItem
+ .addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourByConsensusSecondaryStructureMenuItem_actionPerformed(
+ byConsensusSecondaryStructureMenuItem.isSelected());
+ }
+ });
abovePIDThreshold = new JCheckBoxMenuItem(
MessageManager.getString("label.above_identity_threshold"));
modifyConservation_actionPerformed();
}
});
-
- modifyConsensusSecondaryStructureThreshold = new JMenuItem(MessageManager
- .getString("label.modify_secondary_structure_conservation_threshold"));
- modifyConsensusSecondaryStructureThreshold.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConsensusSecondaryStructureThreshold_actionPerformed();
- }
- });
-
+
+ modifyConsensusSecondaryStructureThreshold = new JMenuItem(
+ MessageManager.getString(
+ "label.modify_secondary_structure_conservation_threshold"));
+ modifyConsensusSecondaryStructureThreshold
+ .addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConsensusSecondaryStructureThreshold_actionPerformed();
+ }
+ });
annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
// TODO Auto-generated method stub
}
-
+
protected void showGroupSSConsensus_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
-
- public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(boolean selected)
+
+ public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(
+ boolean selected)
{
}
protected void modifyConservation_actionPerformed()
{
}
-
+
protected void modifyConsensusSecondaryStructureThreshold_actionPerformed()
{
}
return null;
}
- protected void showOrHideSecondaryStructureForSource(String ssSourceSelection, boolean visible)
+ protected void showOrHideSecondaryStructureForSource(
+ String ssSourceSelection, boolean visible)
{
// TODO Auto-generated method stub
-
+
}
protected void updateShowSecondaryStructureMenu(JMenu showSS,
ButtonGroup ssButtonGroup)
{
// TODO Auto-generated method stub
-
+
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- fontSizeMenu_actionPerformed(e);
+ fontSizeMenu_actionPerformed(e);
}
});
copyItem.setText(MessageManager.getString("action.copy"));
/**
* shows a menu for changing the font
+ *
* @param e
*/
public void fontSizeMenu_actionPerformed(ActionEvent e)
zCombobox.addItem("dim " + i);
}
}
+
public GPCAPanel(int dim)
{
try
zCombobox.addItem("dim " + i);
}
}
+
public GPaSiMapPanel(int dim)
{
try
}
});
JMenuItem outputAlignment = new JMenuItem();
- outputAlignment.setText(
- MessageManager.getString("label.output_alignment"));
+ outputAlignment
+ .setText(MessageManager.getString("label.output_alignment"));
outputAlignment.addActionListener(new ActionListener()
{
@Override
protected JCheckBox conservation = new JCheckBox();
- protected JCheckBox identity = new JCheckBox();
+ protected JCheckBox identity = new JCheckBox();
protected JCheckBox ssConsensus = new JCheckBox();
if (row != null)
{
value[i] = new double[row.length];
- int j = 0;
- for (float oldValue : row)
- {
- value[i][j] = oldValue;
- j++;
- }
+ int j = 0;
+ for (float oldValue : row)
+ {
+ value[i][j] = oldValue;
+ j++;
+ }
}
i++;
}
*/
for (int k = 0; k < in.width(); k++)
{
- if (!Double.isNaN(in.getValue(i,k)) && !Double.isNaN(this.value[k][j]))
- {
+ if (!Double.isNaN(in.getValue(i, k))
+ && !Double.isNaN(this.value[k][j]))
+ {
tmp[i][j] += (in.getValue(i, k) * this.value[k][j]);
- }
+ }
}
}
}
}
/**
- * returns the matrix as a double[][] array
- *
- * @return
- */
+ * returns the matrix as a double[][] array
+ *
+ * @return
+ */
@Override
public double[][] asArray()
{
/**
* Add d to all entries of this matrix
*
- * @param d ~ value to add
+ * @param d
+ * ~ value to add
*/
@Override
public void add(double d)
}
/**
- * Returns a copy in which every value in the matrix is its absolute
+ * Returns a copy in which every value in the matrix is its absolute
*
* @return
*/
{
if (row != null)
{
- mean[i++] = MiscMath.mean(row);
+ mean[i++] = MiscMath.mean(row);
}
}
return mean;
double[] column = getColumn(j);
if (column != null)
{
- mean[j] = MiscMath.mean(column);
+ mean[j] = MiscMath.mean(column);
}
}
return mean;
}
/**
- * return a flattened matrix containing the sum of each column
- *
- * @return
- */
+ * return a flattened matrix containing the sum of each column
+ *
+ * @return
+ */
@Override
public double[] sumCol()
{
double[] column = getColumn(j);
if (column != null)
{
- sum[j] = MiscMath.sum(column);
+ sum[j] = MiscMath.sum(column);
}
- }
+ }
return sum;
}
/**
- * returns the mean value of the complete matrix
- *
- * @return
- */
+ * returns the mean value of the complete matrix
+ *
+ * @return
+ */
@Override
public double mean()
{
{
for (double col : row)
{
- if (!Double.isNaN(col))
- {
- sum += col;
- } else {
- nanCount++;
- }
+ if (!Double.isNaN(col))
+ {
+ sum += col;
+ }
+ else
+ {
+ nanCount++;
+ }
}
}
return sum / (double) (this.rows * this.cols - nanCount);
}
/**
- * fills up a diagonal matrix with its transposed copy
- * !other side should be filled with 0
- * !keeps Double.NaN found in either side
- *
- * TODO check on which side it was diagonal and only do calculations for the other side
- */
+ * fills up a diagonal matrix with its transposed copy !other side should be
+ * filled with 0 !keeps Double.NaN found in either side
+ *
+ * TODO check on which side it was diagonal and only do calculations for the
+ * other side
+ */
@Override
public void fillDiagonal()
{
int n = this.rows;
int m = this.cols;
- MatrixI copy = this.transpose(); // goes through each element in the matrix and
- for (int i = 0; i < n; i++) // adds the value in the transposed copy to the original value
+ MatrixI copy = this.transpose(); // goes through each element in the matrix
+ // and
+ for (int i = 0; i < n; i++) // adds the value in the transposed copy to the
+ // original value
{
for (int j = 0; j < m; j++)
{
- if (i != j)
- {
- this.addValue(i, j, copy.getValue(i,j));
- }
+ if (i != j)
+ {
+ this.addValue(i, j, copy.getValue(i, j));
+ }
}
}
}
/**
- * counts the number of Double.NaN in the matrix
- *
- * @return
- */
+ * counts the number of Double.NaN in the matrix
+ *
+ * @return
+ */
@Override
public int countNaN()
{
{
for (int j = 0; j < this.cols; j++)
{
- if (Double.isNaN(this.getValue(i,j)))
- {
- NaN++;
- }
+ if (Double.isNaN(this.getValue(i, j)))
+ {
+ NaN++;
+ }
}
}
return NaN;
}
/**
- * performs an element-wise addition of this matrix by another matrix ~ this - m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise addition of this matrix by another matrix ~ this -
+ * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI add(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't add a " + m.height() + "x" + m.width() + " to a " + this.rows + "x" + this.cols + " matrix");
+ throw new IllegalArgumentException(
+ "Can't add a " + m.height() + "x" + m.width() + " to a "
+ + this.rows + "x" + this.cols + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i,j) + m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) + m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise subtraction of this matrix by another matrix ~ this - m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise subtraction of this matrix by another matrix ~
+ * this - m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI subtract(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't subtract a " + m.height() + "x" + m.width() + " from a " + this.rows + "x" + this.cols + " matrix");
+ throw new IllegalArgumentException("Can't subtract a " + m.height()
+ + "x" + m.width() + " from a " + this.rows + "x" + this.cols
+ + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i,j) - m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) - m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise multiplication of this matrix by another matrix ~ this * m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise multiplication of this matrix by another matrix ~
+ * this * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI elementwiseMultiply(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't multiply a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix");
+ throw new IllegalArgumentException(
+ "Can't multiply a " + this.rows + "x" + this.cols + " by a "
+ + m.height() + "x" + m.width() + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i, j) * m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) * m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise division of this matrix by another matrix ~ this / m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise division of this matrix by another matrix ~ this /
+ * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI elementwiseDivide(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't divide a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix");
+ throw new IllegalArgumentException(
+ "Can't divide a " + this.rows + "x" + this.cols + " by a "
+ + m.height() + "x" + m.width() + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i, j) / m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) / m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * calculate the root-mean-square for tow matrices
- * @param m ~ other matrix
- *
- * @return
- */
+ * calculate the root-mean-square for tow matrices
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public double rmsd(MatrixI m)
{
}
/**
- * calculates the Frobenius norm of this matrix
- *
- * @return
- */
+ * calculates the Frobenius norm of this matrix
+ *
+ * @return
+ */
@Override
public double norm()
{
{
for (double val : row)
{
- result += Math.pow(val, 2);
+ result += Math.pow(val, 2);
}
}
return Math.sqrt(result);
}
/**
- * returns the sum of all values in this matrix
- *
- * @return
- */
+ * returns the sum of all values in this matrix
+ *
+ * @return
+ */
@Override
public double sum()
{
{
for (double val : row)
{
- sum += (Double.isNaN(val)) ? 0.0 : val;
+ sum += (Double.isNaN(val)) ? 0.0 : val;
}
}
return sum;
}
/**
- * returns the sum-product of this matrix with vector v
- * @param v ~ vector
- *
- * @return
- */
+ * returns the sum-product of this matrix with vector v
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
@Override
public double[] sumProduct(double[] v)
{
if (v.length != cols)
{
- throw new IllegalArgumentException("Vector and matrix do not have the same dimension! (" + v.length + " != " + cols + ")");
+ throw new IllegalArgumentException(
+ "Vector and matrix do not have the same dimension! ("
+ + v.length + " != " + cols + ")");
}
double[] result = new double[rows];
for (int i = 0; i < rows; i++)
double sum = 0;
for (int j = 0; j < row.length; j++)
{
- sum += row[j] * v[j];
+ sum += row[j] * v[j];
}
result[i] = sum;
}
}
/**
- * mirrors columns of the matrix
- *
- * @return
- */
+ * mirrors columns of the matrix
+ *
+ * @return
+ */
@Override
public MatrixI mirrorCol()
{
double[][] result = new double[rows][cols];
for (int i = 0; i < rows; i++)
{
- int k = cols - 1; // reverse col
+ int k = cols - 1; // reverse col
for (int j = 0; j < cols; j++)
{
- result[i][k--] = this.getValue(i,j);
+ result[i][k--] = this.getValue(i, j);
}
}
MatrixI resultMatrix = new Matrix(result);
void setValue(int i, int j, double d);
/**
- * Returns the matrix as a double[][] array
- *
- * @return
- */
+ * Returns the matrix as a double[][] array
+ *
+ * @return
+ */
double[][] asArray();
/**
void multiply(double d);
/**
- * Add d to all entries of this matrix
- *
- * @param d ~ value to add
- */
+ * Add d to all entries of this matrix
+ *
+ * @param d
+ * ~ value to add
+ */
void add(double d);
/**
boolean equals(MatrixI m2, double delta);
/**
- * Returns a copy in which every value in the matrix is its absolute
+ * Returns a copy in which every value in the matrix is its absolute
*/
MatrixI absolute();
double[] meanCol();
/**
- * Returns a flattened matrix containing the sum of each column
- *
- * @return
- */
+ * Returns a flattened matrix containing the sum of each column
+ *
+ * @return
+ */
double[] sumCol();
/**
- * returns the mean value of the complete matrix
- */
+ * returns the mean value of the complete matrix
+ */
double mean();
/**
- * fills up a diagonal matrix with its transposed copy
- * !other side should be filled with either 0 or Double.NaN
- */
+ * fills up a diagonal matrix with its transposed copy !other side should be
+ * filled with either 0 or Double.NaN
+ */
void fillDiagonal();
/**
- * counts the number of Double.NaN in the matrix
- *
- * @return
- */
+ * counts the number of Double.NaN in the matrix
+ *
+ * @return
+ */
int countNaN();
/**
- * performs an element-wise addition of this matrix by another matrix
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise addition of this matrix by another matrix
+ * !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI add(MatrixI m);
/**
- * performs an element-wise subtraction of this matrix by another matrix
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise subtraction of this matrix by another matrix
+ * !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI subtract(MatrixI m);
-
+
/**
- * performs an element-wise multiplication of this matrix by another matrix ~ this * m
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise multiplication of this matrix by another matrix ~
+ * this * m !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI elementwiseMultiply(MatrixI m);
/**
- * performs an element-wise division of this matrix by another matrix ~ this / m
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise division of this matrix by another matrix ~ this /
+ * m !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI elementwiseDivide(MatrixI m);
/**
- * calculates the root-mean-square for two matrices
- * @param m ~ other matrix
- *
- * @return
- */
+ * calculates the root-mean-square for two matrices
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
double rmsd(MatrixI m);
/**
- * calculates the Frobenius norm of this matrix
- *
- * @return
- */
+ * calculates the Frobenius norm of this matrix
+ *
+ * @return
+ */
double norm();
-
+
/**
- * returns the sum of all values in this matrix
- *
- * @return
- */
+ * returns the sum of all values in this matrix
+ *
+ * @return
+ */
double sum();
/**
- * returns the sum-product of this matrix with vector v
- * @param v ~ vector
- *
- * @return
- * @throws IllegalArgumentException
- * if this.cols and v do not have the same length
- */
+ * returns the sum-product of this matrix with vector v
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this.cols and v do not have the same length
+ */
double[] sumProduct(double[] v);
/**
- * mirrors the columns of this matrix
- *
- * @return
- */
+ * mirrors the columns of this matrix
+ *
+ * @return
+ */
MatrixI mirrorCol();
}
/**
* A collection of miscellaneous mathematical operations
+ *
* @AUTHOR MorellThomas
*/
public class MiscMath
{
/**
- * prints an array
- * @param m ~ array
- */
+ * prints an array
+ *
+ * @param m
+ * ~ array
+ */
public static void print(double[] m, String format)
{
System.out.print("[ ");
}
/**
- * calculates the mean of an array
- *
- * @param m ~ array
- * @return
- */
+ * calculates the mean of an array
+ *
+ * @param m
+ * ~ array
+ * @return
+ */
public static double mean(double[] m)
{
double sum = 0;
int nanCount = 0;
for (int i = 0; i < m.length; i++)
{
- if (!Double.isNaN(m[i])) // ignore NaN values in the array
+ if (!Double.isNaN(m[i])) // ignore NaN values in the array
{
sum += m[i];
- } else {
- nanCount++;
+ }
+ else
+ {
+ nanCount++;
}
}
return sum / (double) (m.length - nanCount);
}
/**
- * calculates the sum of an array
- *
- * @param m ~ array
- * @return
- */
+ * calculates the sum of an array
+ *
+ * @param m
+ * ~ array
+ * @return
+ */
public static double sum(double[] m)
{
double sum = 0;
for (int i = 0; i < m.length; i++)
{
- if (!Double.isNaN(m[i])) // ignore NaN values in the array
+ if (!Double.isNaN(m[i])) // ignore NaN values in the array
{
sum += m[i];
}
}
/**
- * calculates the square root of each element in an array
- *
- * @param m ~ array
- *
- * @return
- * TODO
- * make general with function passed -> apply function to each element
- */
+ * calculates the square root of each element in an array
+ *
+ * @param m
+ * ~ array
+ *
+ * @return TODO make general with function passed -> apply function to each
+ * element
+ */
public static double[] sqrt(double[] m)
{
double[] sqrts = new double[m.length];
}
/**
- * calculate element wise multiplication of two arrays with the same length
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseMultiply(byte[] a, double[] b) throws RuntimeException
+ * calculate element wise multiplication of two arrays with the same length
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseMultiply(byte[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
- public static double[] elementwiseMultiply(double[] a, double[] b) throws RuntimeException
+
+ public static double[] elementwiseMultiply(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
- public static byte[] elementwiseMultiply(byte[] a, byte[] b) throws RuntimeException
+
+ public static byte[] elementwiseMultiply(byte[] a, byte[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
+
public static double[] elementwiseMultiply(double[] a, double b)
{
double[] result = new double[a.length];
}
/**
- * calculate element wise division of two arrays ~ a / b
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseDivide(double[] a, double[] b) throws RuntimeException
+ * calculate element wise division of two arrays ~ a / b
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseDivide(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
/**
- * calculate element wise addition of two arrays
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseAdd(double[] a, double[] b) throws RuntimeException
+ * calculate element wise addition of two arrays
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseAdd(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
+
public static double[] elementwiseAdd(double[] a, double b)
{
double[] result = new double[a.length];
}
/**
- * returns true if two arrays are element wise within a tolerance
- *
- * @param a ~ array
- * @param b ~ array
- * @param rtol ~ relative tolerance
- * @param atol ~ absolute tolerance
- * @param equalNAN ~ whether NaN at the same position return true
- *
- * @return
- */
- public static boolean allClose(double[] a, double[] b, double rtol, double atol, boolean equalNAN)
+ * returns true if two arrays are element wise within a tolerance
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ * @param rtol
+ * ~ relative tolerance
+ * @param atol
+ * ~ absolute tolerance
+ * @param equalNAN
+ * ~ whether NaN at the same position return true
+ *
+ * @return
+ */
+ public static boolean allClose(double[] a, double[] b, double rtol,
+ double atol, boolean equalNAN)
{
boolean areEqual = true;
for (int i = 0; i < a.length; i++)
{
- if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN == true -> skip the NaN pair
+ if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN
+ // == true ->
+ // skip the
+ // NaN pair
{
- continue;
+ continue;
}
- if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for the similarity condition -> if not met -> break and return false
+ if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for
+ // the
+ // similarity
+ // condition
+ // -> if not
+ // met ->
+ // break and
+ // return
+ // false
{
- areEqual = false;
- break;
+ areEqual = false;
+ break;
}
}
return areEqual;
}
/**
- * returns the index of the maximum and the maximum value of an array
- *
- * @param a ~ array
- *
- * @return
- */
+ * returns the index of the maximum and the maximum value of an array
+ *
+ * @param a
+ * ~ array
+ *
+ * @return
+ */
public static int[] findMax(int[] a)
{
int max = 0;
{
if (a[i] > max)
{
- max = a[i];
- maxIndex = i;
+ max = a[i];
+ maxIndex = i;
}
}
- return new int[]{maxIndex, max};
+ return new int[] { maxIndex, max };
}
/**
- * returns the dot product of two arrays
- * @param a ~ array a
- * @param b ~ array b
- *
- * @return
- */
+ * returns the dot product of two arrays
+ *
+ * @param a
+ * ~ array a
+ * @param b
+ * ~ array b
+ *
+ * @return
+ */
public static double dot(double[] a, double[] b)
{
if (a.length != b.length)
{
- throw new IllegalArgumentException(String.format("Vectors do not have the same length (%d, %d)!", a.length, b.length));
+ throw new IllegalArgumentException(
+ String.format("Vectors do not have the same length (%d, %d)!",
+ a.length, b.length));
}
double aibi = 0;
}
/**
- * returns the euklidian norm of the vector
- * @param v ~ vector
- *
- * @return
- */
+ * returns the euklidian norm of the vector
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
public static double norm(double[] v)
{
double result = 0;
{
result += Math.pow(i, 2);
}
- return Math.sqrt(result);
+ return Math.sqrt(result);
}
/**
- * returns the number of NaN in the vector
- * @param v ~ vector
- *
- * @return
- */
+ * returns the number of NaN in the vector
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
public static int countNaN(double[] v)
{
int cnt = 0;
{
if (Double.isNaN(i))
{
- cnt++;
+ cnt++;
}
}
return cnt;
}
/**
- * recursively calculates the permutations of total n items with r items per combination
- * according to n!/(n-r)! by only multiplying the relevant terms
- * @param n
- * @param r
- *
- * @return permutations
- */
+ * recursively calculates the permutations of total n items with r items per
+ * combination according to n!/(n-r)! by only multiplying the relevant terms
+ *
+ * @param n
+ * @param r
+ *
+ * @return permutations
+ */
public static long permutations(int n, int r)
{
if (n < r)
long result = 1l;
for (int i = 0; i < r; i++)
{
- result *= (n-i);
+ result *= (n - i);
}
return result;
}
/**
* calculate all unique combinations of n elements into r sized groups
+ *
* @param n
* @param r
*
int result = 1;
for (int i = 0; i < r; i++)
{
- result *= (n-1);
+ result *= (n - 1);
}
return (int) (result / MiscMath.factorial(r));
}
/**
* calculate the factorial of n (n >= 0)
+ *
* @param n
*
* @return
// group has references so set its ID field
jGroup.setId(groupRefs.get(sg));
}
-
- List<String> groupSecondaryStructureSources = sg.getSecondaryStructureSources();
- if(groupSecondaryStructureSources != null && groupSecondaryStructureSources.size()>0) {
+
+ List<String> groupSecondaryStructureSources = sg
+ .getSecondaryStructureSources();
+ if (groupSecondaryStructureSources != null
+ && groupSecondaryStructureSources.size() > 0)
+ {
jGroup.getSecStrProvider().addAll(groupSecondaryStructureSources);
}
-
+
ColourSchemeI colourScheme = sg.getColourScheme();
if (colourScheme != null)
{
}
jGroup.setPidThreshold(groupColourScheme.getThreshold());
-
- if(groupColourScheme.isConsensusSecondaryStructureColouring())
+
+ if (groupColourScheme.isConsensusSecondaryStructureColouring())
{
- jGroup.setSecstrSelected(
- groupColourScheme.isConsensusSecondaryStructureColouring());
+ jGroup.setSecstrSelected(groupColourScheme
+ .isConsensusSecondaryStructureColouring());
jGroup.setSecstrThreshold(groupColourScheme
.getConsensusSecondaryStructureThreshold());
}
}
-
+
jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
jGroup.setDisplayBoxes(sg.getDisplayBoxes());
jGroup.setDisplayText(sg.getDisplayText());
jGroup.getSeq().add(seqHash(seq));
}
}
-
+
// jms.setJGroup(groups);
Object group;
for (JGroup grp : groups)
}
}
view.setPidThreshold(vcs.getThreshold());
-
- if(vcs.isConsensusSecondaryStructureColouring())
+
+ if (vcs.isConsensusSecondaryStructureColouring())
{
- view.setSecstrThreshold(vcs.getConsensusSecondaryStructureThreshold());
+ view.setSecstrThreshold(
+ vcs.getConsensusSecondaryStructureThreshold());
}
}
}
/**
- * Writes PaSiMap viewer attributes and computed values to an XML model object and
- * adds it to the JalviewModel. Any exceptions are reported by logging.
+ * Writes PaSiMap viewer attributes and computed values to an XML model object
+ * and adds it to the JalviewModel. Any exceptions are reported by logging.
* uses the functions from PCA
*/
protected void savePaSiMap(PaSiMapPanel panel, JalviewModel object)
{
- // TODO: this should be merged with above savePCAPanel - otherwise it is essentially redundant code
+ // TODO: this should be merged with above savePCAPanel - otherwise it is
+ // essentially redundant code
try
{
PcaViewer viewer = new PcaViewer();
Console.error("Error saving PaSiMap: " + t.getMessage());
}
}
+
/**
* Stores values from a matrix into an XML element, including (if present) the
* D or E vectors
.setConservationInc(safeInt(jGroup.getConsThreshold()));
sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold(
safeInt(jGroup.getSecstrThreshold()));
-
+
sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
}
else
{
- if (false)//tree.isAnnotationAssociated())
+ if (false)// tree.isAnnotationAssociated())
{
// TODO - resolve annotation IDs against newick tree labels
// then fix up labels so they are human readable
-
- tp = af.showNewickTreeForAnnotation(new NewickFile(tree.getNewick()),
- tree.getTitle(), null, safeInt(tree.getWidth()),
+
+ tp = af.showNewickTreeForAnnotation(
+ new NewickFile(tree.getNewick()), tree.getTitle(),
+ null, safeInt(tree.getWidth()),
safeInt(tree.getHeight()), safeInt(tree.getXpos()),
safeInt(tree.getYpos()));
- } else {
+ }
+ else
+ {
tp = af.showNewickTree(new NewickFile(tree.getNewick()),
- tree.getTitle(), safeInt(tree.getWidth()),
- safeInt(tree.getHeight()), safeInt(tree.getXpos()),
- safeInt(tree.getYpos()));
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
}
}
if (tree.getId() != null)
// recover view properties and display parameters
viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
- viewport.setShowStructureProvider(safeBoolean(view.isShowStructureProviders()));
+ viewport.setShowStructureProvider(
+ safeBoolean(view.isShowStructureProviders()));
viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected()));
final int pidThreshold = safeInt(view.getPidThreshold());
viewport.setThreshold(pidThreshold);
view.isIgnoreGapsinConsensus());
viewport.getResidueShading()
.setConsensus(viewport.getSequenceConsensusHash());
- viewport.getResidueShading()
- .setSSConsensusProfileMap(viewport.getSequenceSSConsensusHash());
+ viewport.getResidueShading().setSSConsensusProfileMap(
+ viewport.getSequenceSSConsensusHash());
if (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
}
if (safeBoolean(view.isSecstrSelected()) && cs != null)
{
- viewport.getResidueShading()
- .setConsensusSecondaryStructureThreshold(
- safeInt(view.getSecstrThreshold()));
+ viewport.getResidueShading().setConsensusSecondaryStructureThreshold(
+ safeInt(view.getSecstrThreshold()));
}
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
private boolean isPasimap(PcaViewer viewer)
{
- return viewer.getTitle().toLowerCase(Locale.ROOT)
- .startsWith("pasimap");
+ return viewer.getTitle().toLowerCase(Locale.ROOT).startsWith("pasimap");
}
+
/**
* Loads any saved PaSiMAp viewers using the function from PCA
*
viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
viewer.isIncludeGaps(),
viewer.isDenominateByShortestLength());
- */
+ */
/*
* create the panel (without computing the PaSiMAp)
PaSiMap pasimap = new PaSiMap(null, scoreModel, null);
PcaDataType pasimapData = viewer.getPcaData();
- MatrixI pairwise = loadDoubleMatrix(pasimapData.getPairwiseMatrix());
+ MatrixI pairwise = loadDoubleMatrix(
+ pasimapData.getPairwiseMatrix());
pasimap.setPairwiseScores(pairwise);
MatrixI result = loadDoubleMatrix(pasimapData.getEigenMatrix());
private HiddenColumns hiddenColumns;
private ProfilesI hconsensus;
-
+
private Map<String, ProfilesI> hSSconsensus;
private Hashtable<String, Object>[] complementConsensus;
}
}
}
-
- if(aa.autoCalculated && aa.label.startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL))
+
+ if (aa.autoCalculated && aa.label
+ .startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL))
{
-
- if(aa.groupRef != null && aa.groupRef.hSSConsensusProfileMap != null
- && aa.groupRef.isShowSequenceLogo()) {
- for (String source : aa.groupRef.hSSConsensusProfileMap.keySet()) {
- if(aa.description.startsWith(source)) {
-
- return AAFrequency.extractProfile(
- aa.groupRef.hSSConsensusProfileMap.get(source).get(column),
- aa.groupRef.getIgnoreGapsConsensus());
+
+ if (aa.groupRef != null && aa.groupRef.hSSConsensusProfileMap != null
+ && aa.groupRef.isShowSequenceLogo())
+ {
+ for (String source : aa.groupRef.hSSConsensusProfileMap.keySet())
+ {
+ if (aa.description.startsWith(source))
+ {
+
+ return AAFrequency
+ .extractProfile(
+ aa.groupRef.hSSConsensusProfileMap.get(source)
+ .get(column),
+ aa.groupRef.getIgnoreGapsConsensus());
+ }
}
}
- }
-
- if(hSSconsensus!=null && aa.groupRef == null) {
- for (String source : hSSconsensus.keySet()) {
- if(aa.description.startsWith(source)) {
-
- return AAFrequency.extractProfile(
- hSSconsensus.get(source).get(column),
- av_ignoreGapsConsensus);
+
+ if (hSSconsensus != null && aa.groupRef == null)
+ {
+ for (String source : hSSconsensus.keySet())
+ {
+ if (aa.description.startsWith(source))
+ {
+
+ return AAFrequency.extractProfile(
+ hSSconsensus.get(source).get(column),
+ av_ignoreGapsConsensus);
+ }
}
}
- }
-
+
}
-
- if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+
+ if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+ {
+ // TODO implement group structure consensus
+ /*
+ * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
+ * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
+ * group selections return StructureFrequency.extractProfile(
+ * aa.groupRef.consensusData[column], aa.groupRef
+ * .getIgnoreGapsConsensus()); }
+ */
+ // TODO extend annotation row to enable dynamic and static profile data
+ // to
+ // be stored
+ if (aa.groupRef == null && aa.sequenceRef == null
+ && hStrucConsensus != null && hStrucConsensus.length > column)
{
- // TODO implement group structure consensus
- /*
- * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
- * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
- * group selections return StructureFrequency.extractProfile(
- * aa.groupRef.consensusData[column], aa.groupRef
- * .getIgnoreGapsConsensus()); }
- */
- // TODO extend annotation row to enable dynamic and static profile data
- // to
- // be stored
- if (aa.groupRef == null && aa.sequenceRef == null
- && hStrucConsensus != null
- && hStrucConsensus.length > column)
- {
- return StructureFrequency.extractProfile(hStrucConsensus[column],
- av_ignoreGapsConsensus);
- }
+ return StructureFrequency.extractProfile(hStrucConsensus[column],
+ av_ignoreGapsConsensus);
}
-
+ }
+
return null;
}
// settings appropriately
// TODO: generalise this to have render styles for consensus/profile
// data
- if (row.groupRef != null &&
- (row == row.groupRef.getConsensus() ||
- (row.groupRef.getSSConsensus(null) !=null && row.groupRef.getSSConsensus(null).contains(row))))
+ if (row.groupRef != null && (row == row.groupRef.getConsensus()
+ || (row.groupRef.getSSConsensus(null) != null
+ && row.groupRef.getSSConsensus(null).contains(row))))
{
renderHistogram = row.groupRef.isShowConsensusHistogram();
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
- else if (row == consensusAnnot
- || row == structConsensusAnnot
- || row == complementConsensusAnnot
- || (ssConsensusAnnot!=null && ssConsensusAnnot.contains(row)))
+ else if (row == consensusAnnot || row == structConsensusAnnot
+ || row == complementConsensusAnnot
+ || (ssConsensusAnnot != null
+ && ssConsensusAnnot.contains(row)))
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
* {profile type, #values, total count, char1, pct1, char2, pct2...}
*/
int profl[] = getProfileFor(_aa, column);
-
-
// just try to draw the logo if profl is not null
if (profl != null && profl[2] != 0)
{
- // TODO do we ever have different profiles for different columns ? Move up to where we set _aa_is_dssp3
+ // TODO do we ever have different profiles for different columns ?
+ // Move up to where we set _aa_is_dssp3
boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
.codonTranslate(s);
colour = profcolour.findColour(codonTranslation.charAt(0),
column, null);
- } else if(_aa_is_dssp3) {
- // TODO - would be nice to get rid of the special 'findSSColour' here ?
+ }
+ else if (_aa_is_dssp3)
+ {
+ // TODO - would be nice to get rid of the special 'findSSColour'
+ // here ?
colour = profcolour.findSSColour(dc[0], column);
}
else
* the consensus data for each column
*/
private ProfilesI consensus;
-
+
/*
* the ss consensus data for each column for each source
*/
-
+
private Map<String, ProfilesI> ssConsensusProfileMap;
/*
* if true, apply shading of colour by conservation
*/
private boolean conservationColouring;
-
+
private boolean consensusSecondaryStructureColouring;
@Override
* setting of the By Conservation slider
*/
private int conservationIncrement = INITIAL_CONSERVATION;
-
+
private int consensusSecondaryStructureThreshold = 30;
public ResidueShader(ColourSchemeI cs)
public void setConsensus(ProfilesI cons)
{
consensus = cons;
-
+
}
/**
}
}
-
+
@Override
- public void setConsensusSecondaryStructureColouring(boolean colourByConsensusSecondaryStructure)
+ public void setConsensusSecondaryStructureColouring(
+ boolean colourByConsensusSecondaryStructure)
{
-
+
consensusSecondaryStructureColouring = colourByConsensusSecondaryStructure;
-
+
}
/**
{
consensusSecondaryStructureThreshold = i;
}
-
+
@Override
public int getConsensusSecondaryStructureThreshold()
{
return consensusSecondaryStructureThreshold;
}
-
+
/**
* @see jalview.renderer.ResidueShaderI#getThreshold()
*/
return colour;
}
-
+
@Override
public Color findSSColour(char symbol, int position)
{
return Color.white; // Colour is 'None'
}
- Color colour = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
-
+ Color colour = AlignmentUtils
+ .getSecondaryStructureAnnotationColour(symbol);
+
/*
* apply PID threshold and consensus fading if in force
*/
{
colour = Color.white;
}
-
- if(consensusSecondaryStructureColouring)
+
+ if (consensusSecondaryStructureColouring)
{
colour = applyByConsensusSecondaryStructure(colour, column);
}
return ColorUtils.bleachColour(currentColour, bleachFactor);
}
-
-
- protected Color applyByConsensusSecondaryStructure(Color currentColour, int column)
+
+ protected Color applyByConsensusSecondaryStructure(Color currentColour,
+ int column)
{
- if (ssConsensusProfileMap == null &&
- ssConsensusProfileMap.get(Constants.SS_ALL_PROVIDERS) == null)
+ if (ssConsensusProfileMap == null && ssConsensusProfileMap
+ .get(Constants.SS_ALL_PROVIDERS) == null)
{
return currentColour;
}
-
- ProfilesI consensusSSProfileForAllSources =
- ssConsensusProfileMap.get(Constants.SS_ALL_PROVIDERS);
+
+ ProfilesI consensusSSProfileForAllSources = ssConsensusProfileMap
+ .get(Constants.SS_ALL_PROVIDERS);
ProfileI profile = consensusSSProfileForAllSources.get(column);
-
- if(profile != null)
- {
- float pid = profile.getSSPercentageIdentity(ignoreGaps);
- if(pid == 0) {
- return Color.white;
- }
+ if (profile != null)
+ {
+ float pid = profile.getSSPercentageIdentity(ignoreGaps);
+
+ if (pid == 0)
+ {
+ return Color.white;
+ }
- float bleachFactor = 1f - (pid/100);
- bleachFactor *= (consensusSecondaryStructureThreshold/20);
+ float bleachFactor = 1f - (pid / 100);
+ bleachFactor *= (consensusSecondaryStructureThreshold / 20);
+
+ return ColorUtils.bleachColour(currentColour, bleachFactor);
- return ColorUtils.bleachColour(currentColour, bleachFactor);
-
}
-
+
return currentColour;
}
return ssConsensusProfileMap;
}
- public void setSSConsensusProfileMap(Map<String, ProfilesI> ssConsensusProfileMap)
+ public void setSSConsensusProfileMap(
+ Map<String, ProfilesI> ssConsensusProfileMap)
{
this.ssConsensusProfileMap = ssConsensusProfileMap;
}
{
public abstract void setConsensus(ProfilesI cons);
-
- public abstract void setSSConsensusProfileMap(Map<String, ProfilesI> ssConsensusProfileMap);
+
+ public abstract void setSSConsensusProfileMap(
+ Map<String, ProfilesI> ssConsensusProfileMap);
public abstract boolean conservationApplied();
{
return false;
}
+
public String toRuleRep()
{
makeColours();
- HashMap<String, String> cols=new HashMap();
- for (String res:ResidueProperties.aa) {
+ HashMap<String, String> cols = new HashMap();
+ for (String res : ResidueProperties.aa)
+ {
StringBuilder sb = new StringBuilder();
-
- int rnum=ResidueProperties.aaIndex[res.charAt(0)];
- if (rnum<0 || rnum>=residueColour.length)
+
+ int rnum = ResidueProperties.aaIndex[res.charAt(0)];
+ if (rnum < 0 || rnum >= residueColour.length)
{
continue;
}
-
+
ConsensusColour cc = residueColour[rnum];
- if (cc==null)
+ if (cc == null)
{
continue;
}
- //sb.append("Residue "+res+" ("+rnum+")");
- //sb.append("\t");
+ // sb.append("Residue "+res+" ("+rnum+")");
+ // sb.append("\t");
sb.append(cc.c.toString());
- double f=0;
+ double f = 0;
sb.append("\t");
- for (Consensus cons: cc.cons) {
- if (cons.threshold==0 || f!=cons.threshold)
+ for (Consensus cons : cc.cons)
+ {
+ if (cons.threshold == 0 || f != cons.threshold)
{
- if (f!=0)
+ if (f != 0)
{
- sb.append("}, {");
- } else {
- sb.append("{");
+ sb.append("}, {");
+ }
+ else
+ {
+ sb.append("{");
}
- sb.append(cons.threshold);
- sb.append(",");
- f=cons.threshold;
- } else {
+ sb.append(cons.threshold);
+ sb.append(",");
+ f = cons.threshold;
+ }
+ else
+ {
sb.append(",");
}
sb.append(cons.maskstr);
}
sb.append("}");
- String clxrep=sb.toString();
+ String clxrep = sb.toString();
String xres = cols.get(clxrep);
- if (xres==null) { xres = "";}
- xres+=res;
+ if (xres == null)
+ {
+ xres = "";
+ }
+ xres += res;
cols.put(clxrep, xres);
}
StringBuilder sb = new StringBuilder();
- for (String clxrep:cols.keySet())
+ for (String clxrep : cols.keySet())
{
sb.append(cols.get(clxrep));
sb.append("\t");
sb.append(clxrep);
sb.append("\n");
-
+
}
return sb.toString();
}
public static final int[] nucleotideIndex;
public static final int[] purinepyrimidineIndex;
-
+
public static final int[] secondaryStructureIndex;
public static final Map<String, Integer> aa3Hash = new HashMap<>();
purinepyrimidineIndex['N'] = 2;
purinepyrimidineIndex['n'] = 2;
}
-
+
static
{
secondaryStructureIndex = new int[255];
for (int i = 0; i < 255; i++)
{
- secondaryStructureIndex[i] = 3;
+ secondaryStructureIndex[i] = 3;
}
secondaryStructureIndex['H'] = 0;
Color.white, // all other nucleotides
Color.white // Gap
};
-
- //Secondary structure
- public static final Color[] secondarystructure = { Color.red, // H
- Color.green, // E
- Color.gray // C
- };
+
+ // Secondary structure
+ public static final Color[] secondarystructure = { Color.red, // H
+ Color.green, // E
+ Color.gray // C
+ };
// Zappo
public static final Color[] zappo = { Color.pink, // A
StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
-
- //JAL-4392 TODO: Unable to match PDBProvider with Annotation without matching struct file path
+
+ // JAL-4392 TODO: Unable to match PDBProvider with Annotation without
+ // matching struct file path
String ssAnnotDescriptionInPDB = null;
- String ssStructFilePathNameInPDB = pdb.getInFile(); //Structure file name in PDB data model
- //Secondary structure annotations in pdb data model
- AlignmentAnnotation[] ssAnnotationsInPDB = pdb.getSeqs().get(0).getAnnotation(Constants.SS_ANNOTATION_LABEL);
- if(ssAnnotationsInPDB != null && ssAnnotationsInPDB.length>0) {
+ String ssStructFilePathNameInPDB = pdb.getInFile(); // Structure file name
+ // in PDB data model
+ // Secondary structure annotations in pdb data model
+ AlignmentAnnotation[] ssAnnotationsInPDB = pdb.getSeqs().get(0)
+ .getAnnotation(Constants.SS_ANNOTATION_LABEL);
+ if (ssAnnotationsInPDB != null && ssAnnotationsInPDB.length > 0)
+ {
ssAnnotDescriptionInPDB = ssAnnotationsInPDB[0].description;
}
-
+
// Match the PDB entry using file path in the pdb data model and get the
// provider
if (ssStructFilePathNameInPDB != null
// Add provider value as property to the ss annotation
if (provider != null)
{
- // TODO - JAL-2880 JAL-4441 this should be applied to all structure derived annotations, not just secondary structure!
+ // TODO - JAL-2880 JAL-4441 this should be applied to all structure
+ // derived annotations, not just secondary structure!
AlignmentAnnotation[] ssAnnotList = ds
.getAnnotation(Constants.SS_ANNOTATION_LABEL);
if (ssAnnotList != null)
}
}
}
-
-
+
if (forStructureView)
{
for (StructureMapping sm : seqToStrucMapping)
*/
public class Constants
{
-
- //character used to represent secondary structures
+
+ // character used to represent secondary structures
public static final char HELIX = 'H';
+
public static final char SHEET = 'E';
+
public static final char COIL = 'C';
- //label in secondary structure annotation data model from 3d structures
+ // label in secondary structure annotation data model from 3d structures
public static final String SS_ANNOTATION_LABEL = "Secondary Structure";
-
- //label in secondary structure annotation data model from JPred
- public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred";
-
+
+ // label in secondary structure annotation data model from JPred
+ public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred";
+
public static final Map<String, String> SECONDARY_STRUCTURE_LABELS = new HashMap<>();
- static {
- SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures");
- SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred");
- // Add other secondary structure labels here if needed
- }
-
- public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER";
-
- //generic secondary structure provider options
- public static final String SS_ALL_PROVIDERS = "All";
+ static
+ {
+ SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures");
+ SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred");
+ // Add other secondary structure labels here if needed
+ }
+
+ public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER";
+
+ // generic secondary structure provider options
+ public static final String SS_ALL_PROVIDERS = "All";
+
public static final String SS_NONE_PROVIDER = "None";
-
- //Secondary structure consensus label
+
+ // Secondary structure consensus label
public static final String SECONDARY_STRUCTURE_CONSENSUS_LABEL = "Secondary Structure Consensus";
}
{
return viewStyle.getAbovePIDThreshold();
}
-
+
@Override
public boolean getByConsensusSecondaryStructureSelected()
{
public int getIncrement()
{
return viewStyle.getIncrement();
- }
-
+ }
+
/**
* @param inc
* @see jalview.api.ViewStyleI#setConsensusSecondaryStructureThreshold(int)
{
viewStyle.setConsensusSecondaryStructureThreshold(val);
}
-
+
/**
* @return
* @see jalview.api.ViewStyleI#getConsensusSecondaryStructureThreshold()
public int getConsensusSecondaryStructureThreshold()
{
return viewStyle.getConsensusSecondaryStructureThreshold();
- }
-
+ }
/**
* @param b
{
viewStyle.setAbovePIDThreshold(b);
}
-
+
@Override
public void setByConsensusSecondaryStructureSelected(boolean b)
{
}
protected AlignmentAnnotation consensus;
-
+
protected List<AlignmentAnnotation> secondaryStructureConsensus;
protected AlignmentAnnotation complementConsensus;
protected AlignmentAnnotation quality;
protected AlignmentAnnotation[] groupConsensus;
-
+
protected AlignmentAnnotation[] groupSSConsensus;
protected AlignmentAnnotation[] groupConservation;
* results of alignment consensus analysis for visible portion of view
*/
protected ProfilesI hconsensus = null;
-
+
protected Map<String, ProfilesI> hSSConsensusProfileMap = null;
-
-
/**
* results of cDNA complement consensus visible portion of view
{
hconservation = cons;
}
-
+
@Override
public List<String> getSecondaryStructureSources()
{
{
viewStyle.setSecondaryStructureSources(secondaryStructureSources);
}
-
+
protected void setSecondaryStructureSources(AlignmentAnnotation[] aa)
{
List<String> sources = null;
-
- if(aa!=null) {
+
+ if (aa != null)
+ {
sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa);
- if(sources != null) {
- sources.add(0,Constants.SS_ALL_PROVIDERS);
+ if (sources != null)
+ {
+ sources.add(0, Constants.SS_ALL_PROVIDERS);
viewStyle.setSecondaryStructureSources(sources);
}
}
{
this.hconsensus = hconsensus;
}
-
+
@Override
- public void setSequenceSSConsensusHash(Map<String, ProfilesI> hSSConsensusProfileMap)
+ public void setSequenceSSConsensusHash(
+ Map<String, ProfilesI> hSSConsensusProfileMap)
{
this.hSSConsensusProfileMap = hSSConsensusProfileMap;
}
-
+
@Override
public void setComplementConsensusHash(
Hashtable<String, Object>[] hconsensus)
{
return hSSConsensusProfileMap;
}
-
@Override
public Hashtable<String, Object>[] getComplementConsensusHash()
return consensus;
}
-
@Override
public List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation()
{
return secondaryStructureConsensus;
}
-
@Override
public AlignmentAnnotation getAlignmentGapAnnotation()
}
}
}
-
-
-
/**
* trigger update of Secondary Structure consensus annotation
return;
}
List<String> ssSources = viewStyle.getSecondaryStructureSources();
- if (secondaryStructureConsensus.size() != ssSources.size()) {
-
- for(String source : ssSources) {
+ if (secondaryStructureConsensus.size() != ssSources.size())
+ {
+
+ for (String source : ssSources)
+ {
boolean ssConsensusForSourcePresent = false;
- for(AlignmentAnnotation aa : secondaryStructureConsensus) {
- if(aa.description.startsWith(source)) {
+ for (AlignmentAnnotation aa : secondaryStructureConsensus)
+ {
+ if (aa.description.startsWith(source))
+ {
ssConsensusForSourcePresent = true;
break;
}
}
-
- if(!ssConsensusForSourcePresent) {
- AlignmentAnnotation ssConsensus = new AlignmentAnnotation(MessageManager.getString("label.ssconsensus_label") + " "+source,
- source + " " + MessageManager.getString("label.ssconsensus_descr"),
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+
+ if (!ssConsensusForSourcePresent)
+ {
+ AlignmentAnnotation ssConsensus = new AlignmentAnnotation(
+ MessageManager.getString("label.ssconsensus_label") + " "
+ + source,
+ source + " "
+ + MessageManager
+ .getString("label.ssconsensus_descr"),
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
ssConsensus.hasText = true;
ssConsensus.autoCalculated = true;
{
ssConsensus.visible = true;
alignment.addAnnotation(ssConsensus);
-
+
}
}
}
}
- if (calculator
- .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class) == null)
+ if (calculator.getRegisteredWorkersOfClass(
+ SecondaryStructureConsensusThread.class) == null)
{
- calculator.registerWorker(new SecondaryStructureConsensusThread(this, ap));
+ calculator.registerWorker(
+ new SecondaryStructureConsensusThread(this, ap));
}
ap.adjustAnnotationHeight();
-
}
// --------START Structure Conservation
* should consensus rows be shown for groups
*/
protected boolean showGroupConsensus = false;
-
protected boolean showGroupSSConsensus = false;
* should consensus profile be rendered by default
*/
protected boolean showSequenceLogo = false;
-
+
/**
* should consensus profile be rendered normalised to row height
*/
* should consensus histograms be rendered by default
*/
protected boolean showConsensusHistogram = true;
-
+
/**
* @return the showConsensusProfile
*/
{
return showSequenceLogo;
}
-
+
/**
* @param showSequenceLogo
* the new value
calculator.updateAnnotationFor(ConsensusThread.class);
calculator.updateAnnotationFor(ComplementConsensusThread.class);
calculator.updateAnnotationFor(StrucConsensusThread.class);
-
- //to do
- calculator.updateAnnotationFor(SecondaryStructureConsensusThread.class);
+ // to do
+
+ calculator
+ .updateAnnotationFor(SecondaryStructureConsensusThread.class);
}
this.showSequenceLogo = showSequenceLogo;
}
-
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
{
return showGroupConsensus;
}
-
+
public boolean isShowGroupSSConsensus()
{
return showGroupSSConsensus;
}
-
/**
* @param showGroupConsensus
* the showGroupConsensus to set
{
this.showGroupConsensus = showGroupConsensus;
}
-
+
public void setShowGroupSSConsensus(boolean showGroupSSConsensus)
{
this.showGroupSSConsensus = showGroupSSConsensus;
}
-
+
/**
* @param showSSConsensus
* the showSSConsensus to set
{
this.showSSConsensus = showSSConsensus;
}
-
+
/**
*
* @return flag to indicate if the consensus histogram should be rendered by
protected boolean showQuality = true;
- protected boolean showConsensus = true;
+ protected boolean showConsensus = true;
protected boolean showSSConsensus = true;
setSecondaryStructureSources(alignment.getAlignmentAnnotation());
List<String> secondaryStructureSources = getSecondaryStructureSources();
- if(secondaryStructureSources!=null) {
+ if (secondaryStructureSources != null)
+ {
secondaryStructureConsensus = new ArrayList<AlignmentAnnotation>();
- for (String ssSource : secondaryStructureSources) {
-
- AlignmentAnnotation ssConsensus = new AlignmentAnnotation(MessageManager.getString("label.ssconsensus_label") + " "+ssSource,
- ssSource + " " + MessageManager.getString("label.ssconsensus_descr"),
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ for (String ssSource : secondaryStructureSources)
+ {
+
+ AlignmentAnnotation ssConsensus = new AlignmentAnnotation(
+ MessageManager.getString("label.ssconsensus_label") + " "
+ + ssSource,
+ ssSource + " "
+ + MessageManager
+ .getString("label.ssconsensus_descr"),
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
secondaryStructureConsensus.add(ssConsensus);
}
-
+
}
-
+
initConsensus(consensus);
initSSConsensus(secondaryStructureConsensus);
initGapCounts();
}
}
-
/**
* If this is a protein alignment and there are mappings to cDNA, adds the
* cDNA consensus annotation and returns true, else returns false.
alignment.addAnnotation(aa);
}
}
-
- private void initSSConsensus(List<AlignmentAnnotation> secondaryStructureConsensuses)
+
+ private void initSSConsensus(
+ List<AlignmentAnnotation> secondaryStructureConsensuses)
{
- if(secondaryStructureConsensuses == null) {
+ if (secondaryStructureConsensuses == null)
+ {
return;
}
- for(AlignmentAnnotation aa : secondaryStructureConsensuses) {
+ for (AlignmentAnnotation aa : secondaryStructureConsensuses)
+ {
aa.hasText = true;
aa.autoCalculated = true;
-
+
if (showSSConsensus)
{
alignment.addAnnotation(aa);
}
-
+
}
}
updateCalcs = true;
alignment.addAnnotation(sg.getConsensus(), 0);
}
- if(sscons)
- {
+ if (sscons)
+ {
updateCalcs = true;
List<String> secondaryStructureSources = getSecondaryStructureSources();
- if(secondaryStructureSources !=null) {
- List<AlignmentAnnotation> ssAa = sg.getSSConsensus(secondaryStructureSources);
- if(ssAa != null) {
- for(AlignmentAnnotation aa : ssAa) {
+ if (secondaryStructureSources != null)
+ {
+ List<AlignmentAnnotation> ssAa = sg
+ .getSSConsensus(secondaryStructureSources);
+ if (ssAa != null)
+ {
+ for (AlignmentAnnotation aa : ssAa)
+ {
// Setting annotation visibility to true for the secondary
// structure consensus for all providers
if (aa.label.contains(Constants.SS_ALL_PROVIDERS))
{
aa.visible = true;
}
- alignment.addAnnotation(aa, 0);
+ alignment.addAnnotation(aa, 0);
}
}
}
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
-
- //to do jal-4386
+
+ // to do jal-4386
public SequenceI getSSConsensusSeq()
{
if (secondaryStructureConsensus == null)
return null;
}
StringBuffer seqs = new StringBuffer();
-// for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++)
-// {
-// Annotation annotation = secondaryStructureConsensus.annotations[i];
-// if (annotation != null)
-// {
-// String description = annotation.description;
-// if (description != null && description.startsWith("["))
-// {
-// // consensus is a tie - just pick the first one
-// seqs.append(description.charAt(1));
-// }
-// else
-// {
-// seqs.append(annotation.displayCharacter);
-// }
-// }
-// }
+ // for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++)
+ // {
+ // Annotation annotation = secondaryStructureConsensus.annotations[i];
+ // if (annotation != null)
+ // {
+ // String description = annotation.description;
+ // if (description != null && description.startsWith("["))
+ // {
+ // // consensus is a tie - just pick the first one
+ // seqs.append(description.charAt(1));
+ // }
+ // else
+ // {
+ // seqs.append(annotation.displayCharacter);
+ // }
+ // }
+ // }
SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString());
sq.setDescription("Percentage Identity Sec Str Consensus "
* @param modelName
* @param params
*/
- public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
- ScoreModelI modelName)
+ public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs,
+ boolean nuc, ScoreModelI modelName)
{
inputData = seqData;
seqs = sqs;
}
/**
- * Performs the PaSiMap calculation (in the same thread) and extracts result data
- * needed for visualisation by PaSiMapPanel
+ * Performs the PaSiMap calculation (in the same thread) and extracts result
+ * data needed for visualisation by PaSiMapPanel
*/
public void calculate(PairwiseAlignPanel pap)
{
top = width;
points = new Vector<>();
- Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
+ Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3,
+ 1);
for (int i = 0; i < height; i++)
{
/**
* Updates the 3D coordinates for the list of points to the given dimensions.
* Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
- * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
- * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
+ * Note - pasimap.getComponents starts counting the spectrum from rank-2 to
+ * zero, rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1
+ * ..)
*
* @param dim1
* @param dim2
csv.append("\"" + seqs[s].getName() + "\"");
if (!transformed)
{
- double[] fl = pasimap.component(s);
- for (int d = fl.length - 1; d >= 0; d--)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
- } else {
+ double[] fl = pasimap.component(s);
+ for (int d = fl.length - 1; d >= 0; d--)
+ {
+ csv.append(",");
+ csv.append(fl[d]);
+ }
+ }
+ else
+ {
Point p = points.get(s).coord;
csv.append(",").append(p.x);
csv.append(",").append(p.y);
private boolean colourByReferenceSeq = false;
boolean conservationColourSelected = false;
-
+
boolean byConsensusSecondaryStructureSelected = false;
/**
private boolean displayReferenceSeq = false;
private int increment;
-
+
private int consensusSecondaryStructureThreshold;
/**
setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups());
setColourByReferenceSeq(vs.isColourByReferenceSeq());
setColourText(vs.getColourText());
- setByConsensusSecondaryStructureSelected(vs.getByConsensusSecondaryStructureSelected());
- setConsensusSecondaryStructureThreshold(vs.getConsensusSecondaryStructureThreshold());
+ setByConsensusSecondaryStructureSelected(
+ vs.getByConsensusSecondaryStructureSelected());
+ setConsensusSecondaryStructureThreshold(
+ vs.getConsensusSecondaryStructureThreshold());
setConservationColourSelected(vs.isConservationColourSelected());
setConservationSelected(vs.getConservationSelected());
setDisplayReferenceSeq(vs.isDisplayReferenceSeq());
&& getColourText() == vs.getColourText()
&& isConservationColourSelected() == vs
.isConservationColourSelected()
- && getByConsensusSecondaryStructureSelected() == vs.getByConsensusSecondaryStructureSelected()
+ && getByConsensusSecondaryStructureSelected() == vs
+ .getByConsensusSecondaryStructureSelected()
&& getConservationSelected() == vs.getConservationSelected()
&& isDisplayReferenceSeq() == vs.isDisplayReferenceSeq()
&& getFontSize() == vs.getFontSize()
&& getFontStyle() == vs.getFontStyle()
&& getIdWidth() == vs.getIdWidth()
&& getIncrement() == vs.getIncrement()
- && getConsensusSecondaryStructureThreshold() == vs.getConsensusSecondaryStructureThreshold()
+ && getConsensusSecondaryStructureThreshold() == vs
+ .getConsensusSecondaryStructureThreshold()
&& isRenderGaps() == vs.isRenderGaps()
&& isRightAlignIds() == vs.isRightAlignIds()
&& getScaleAboveWrapped() == vs.getScaleAboveWrapped()
&& isUpperCasebold() == vs.isUpperCasebold()
&& getWrapAlignment() == vs.getWrapAlignment()
&& getWrappedWidth() == vs.getWrappedWidth()
- && getSecondaryStructureSources() == vs.getSecondaryStructureSources()
+ && getSecondaryStructureSources() == vs
+ .getSecondaryStructureSources()
&& isShowStructureProvider() == vs.isShowStructureProvider());
/*
* and compare non-primitive types; syntax below will match null with null
private boolean showComplementFeatures;
private boolean showComplementFeaturesOnTop;
-
+
/**
- * secondary structure annotation rows shown in the view
- */
- private List<String> secondaryStructureSources = List.of( new String[0] );
+ * secondary structure annotation rows shown in the view
+ */
+ private List<String> secondaryStructureSources = List.of(new String[0]);
private boolean showStructureProvider;
{
return byConsensusSecondaryStructureSelected;
}
+
/**
* DOCUMENT ME!
*
{
return threshold;
}
-
+
@Override
public int getConsensusSecondaryStructureThreshold()
{
return consensusSecondaryStructureThreshold;
}
-
/**
* @return the thresholdTextColour
{
abovePIDThreshold = b;
}
-
+
@Override
public void setByConsensusSecondaryStructureSelected(boolean b)
{
{
increment = inc;
}
-
+
/**
*
* @param val
{
consensusSecondaryStructureThreshold = val;
}
-
/**
* DOCUMENT ME!
{
return showComplementFeaturesOnTop;
}
-
+
@Override
public List<String> getSecondaryStructureSources()
{
}
@Override
- public void setSecondaryStructureSources(List<String> secondaryStructureSources)
+ public void setSecondaryStructureSources(
+ List<String> secondaryStructureSources)
{
this.secondaryStructureSources = secondaryStructureSources;
}
@Override
public void setShowStructureProvider(boolean showStructureProvider)
{
- this.showStructureProvider=showStructureProvider;
+ this.showStructureProvider = showStructureProvider;
}
+
@Override
public boolean isShowStructureProvider()
{
calcMan.workerComplete(this);
return;
}
-
+
setSecondaryStructureSources();
eraseSSConsensus(aWidth);
computeSSConsensus(alignment);
protected void eraseSSConsensus(int aWidth)
{
List<AlignmentAnnotation> ssConsensuses = getSSConsensusAnnotation();
- for(AlignmentAnnotation ssConsensus : ssConsensuses) {
+ for (AlignmentAnnotation ssConsensus : ssConsensuses)
+ {
if (ssConsensus != null)
{
ssConsensus.annotations = new Annotation[aWidth];
SequenceI[] aseqs = getSequences();
int width = alignment.getWidth();
Map<String, ProfilesI> hSSConsensusProfileMap = new HashMap<String, ProfilesI>();
- List <String> ssSources = getSecondaryStructureSources();
- for(String ssSource : ssSources) {
- ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0, width,
- true, ssSource);
+ List<String> ssSources = getSecondaryStructureSources();
+ for (String ssSource : ssSources)
+ {
+ ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0,
+ width, true, ssSource);
hSSConsensusProfileMap.put(ssSource, hSSConsensus);
}
-
alignViewport.setSequenceSSConsensusHash(hSSConsensusProfileMap);
setColourSchemeConsensus(hSSConsensusProfileMap);
/**
* @param hconsensus
*/
- protected void setColourSchemeConsensus(Map<String, ProfilesI> ssConsensusProfileMap)
+ protected void setColourSchemeConsensus(
+ Map<String, ProfilesI> ssConsensusProfileMap)
{
ResidueShaderI cs = alignViewport.getResidueShading();
if (cs != null)
*/
protected List<AlignmentAnnotation> getSSConsensusAnnotation()
{
- return alignViewport.getAlignmentSecondaryStructureConsensusAnnotation();
+ return alignViewport
+ .getAlignmentSecondaryStructureConsensusAnnotation();
}
-
+
/**
* Get the Consensus annotation for the alignment
*
protected void setSecondaryStructureSources()
{
List<String> sources = null;
- AlignmentAnnotation[] aa = alignViewport.getAlignment().getAlignmentAnnotation();
- if(aa!=null) {
+ AlignmentAnnotation[] aa = alignViewport.getAlignment()
+ .getAlignmentAnnotation();
+ if (aa != null)
+ {
sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa);
- if(sources != null) {
+ if (sources != null)
+ {
sources.add(0, Constants.SS_ALL_PROVIDERS);
alignViewport.setSecondaryStructureSources(sources);
}
}
}
-
+
protected List<String> getSecondaryStructureSources()
{
return alignViewport.getSecondaryStructureSources();
{
List<AlignmentAnnotation> ssConsensuses = getSSConsensusAnnotation();
Map<String, ProfilesI> ssConsensusProfileMap = getViewportSSConsensus();
- for(AlignmentAnnotation ssConsensus : ssConsensuses) {
+ for (AlignmentAnnotation ssConsensus : ssConsensuses)
+ {
ProfilesI ssConsensusProfile = null;
- for(String source: ssConsensusProfileMap.keySet()) {
- if(ssConsensus.description.startsWith(source)) {
+ for (String source : ssConsensusProfileMap.keySet())
+ {
+ if (ssConsensus.description.startsWith(source))
+ {
ssConsensusProfile = ssConsensusProfileMap.get(source);
break;
}
}
- if(ssConsensusProfile==null) {
- continue;
- }
- if (immediate || !calcMan.isWorking(this) && ssConsensus != null
- && ssConsensusProfile != null)
- {
- if(ssConsensusProfile.get(0)!=null)
- ssConsensus.setNoOfSequencesIncluded(ssConsensusProfile.get(0).getSeqWithSSCount());
- deriveSSConsensus(ssConsensus, ssConsensusProfile);
- AlignmentAnnotation gap = getGapAnnotation();
- if (gap != null)
+ if (ssConsensusProfile == null)
{
- deriveGap(gap, ssConsensusProfile);
+ continue;
+ }
+ if (immediate || !calcMan.isWorking(this) && ssConsensus != null
+ && ssConsensusProfile != null)
+ {
+ if (ssConsensusProfile.get(0) != null)
+ ssConsensus.setNoOfSequencesIncluded(
+ ssConsensusProfile.get(0).getSeqWithSSCount());
+ deriveSSConsensus(ssConsensus, ssConsensusProfile);
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ deriveGap(gap, ssConsensusProfile);
+ }
}
- }
}
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "alcodon",
- "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+public class AlcodonFrame
+{
+
+ protected List<AlcodonFrame.Alcodon> alcodon;
+
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
+
+ /**
+ * Gets the value of the alcodon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alcodon property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAlcodon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.Alcodon }
+ * </p>
+ *
+ *
+ * @return The value of the alcodon property.
+ */
+ public List<AlcodonFrame.Alcodon> getAlcodon()
+ {
+ if (alcodon == null)
+ {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ return this.alcodon;
+ }
+
+ /**
+ * Gets the value of the alcodMap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alcodMap property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAlcodMap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.AlcodMap }
+ * </p>
+ *
+ *
+ * @return The value of the alcodMap property.
+ */
+ public List<AlcodonFrame.AlcodMap> getAlcodMap()
+ {
+ if (alcodMap == null)
+ {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ return this.alcodMap;
+ }
- protected List<AlcodonFrame.Alcodon> alcodon;
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ * </sequence>
+ * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "mapping" })
+ public static class AlcodMap
+ {
/**
- * Gets the value of the alcodon property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodon property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAlcodon().add(newItem);
- * </pre>
+ * a Mapping entry and an associated protein sequence
*
+ */
+ @XmlElement(name = "Mapping", required = true)
+ protected Mapping mapping;
+
+ /**
+ * internal jalview id for the dnasq for this mapping.
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.Alcodon }
- * </p>
+ */
+ @XmlAttribute(name = "dnasq", required = true)
+ protected String dnasq;
+
+ /**
+ * a Mapping entry and an associated protein sequence
*
+ * @return possible object is {@link Mapping }
*
- * @return
- * The value of the alcodon property.
*/
- public List<AlcodonFrame.Alcodon> getAlcodon() {
- if (alcodon == null) {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- return this.alcodon;
+ public Mapping getMapping()
+ {
+ return mapping;
}
/**
- * Gets the value of the alcodMap property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodMap property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAlcodMap().add(newItem);
- * </pre>
- *
+ * Sets the value of the mapping property.
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.AlcodMap }
- * </p>
+ * @param value
+ * allowed object is {@link Mapping }
*
- *
- * @return
- * The value of the alcodMap property.
+ * @see #getMapping()
*/
- public List<AlcodonFrame.AlcodMap> getAlcodMap() {
- if (alcodMap == null) {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- return this.alcodMap;
+ public void setMapping(Mapping value)
+ {
+ this.mapping = value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * internal jalview id for the dnasq for this mapping.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence>
- * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getDnasq()
+ {
+ return dnasq;
+ }
+
+ /**
+ * Sets the value of the dnasq property.
*
+ * @param value
+ * allowed object is {@link String }
*
+ * @see #getDnasq()
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapping"
- })
- public static class AlcodMap {
+ public void setDnasq(String value)
+ {
+ this.dnasq = value;
+ }
- /**
- * a Mapping entry and an associated protein
- * sequence
- *
- */
- @XmlElement(name = "Mapping", required = true)
- protected Mapping mapping;
- /**
- * internal jalview id for the dnasq for this
- * mapping.
- *
- */
- @XmlAttribute(name = "dnasq", required = true)
- protected String dnasq;
+ }
- /**
- * a Mapping entry and an associated protein
- * sequence
- *
- * @return
- * possible object is
- * {@link Mapping }
- *
- */
- public Mapping getMapping() {
- return mapping;
- }
+ /**
+ * specifies a series of aligned codons from an associated DNA sequence
+ * alignment that when translated correspond to columns of a peptide
+ * alignment. Element may have either all pos1,2,3 attributes specified, or
+ * none at all (indicating a gapped column with no translated peptide).
+ *
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Alcodon
+ {
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link Mapping }
- *
- * @see #getMapping()
- */
- public void setMapping(Mapping value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
- /**
- * internal jalview id for the dnasq for this
- * mapping.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDnasq() {
- return dnasq;
- }
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
- /**
- * Sets the value of the dnasq property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getDnasq()
- */
- public void setDnasq(String value) {
- this.dnasq = value;
- }
+ @XmlAttribute(name = "pos3")
+ protected BigInteger pos3;
+ /**
+ * Gets the value of the pos1 property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPos1()
+ {
+ return pos1;
}
-
/**
- * specifies a series of aligned codons from an
- * associated DNA sequence alignment that when translated
- * correspond to columns of a peptide alignment.
- * Element may have
- * either all pos1,2,3 attributes specified, or none at all
- * (indicating a gapped column with no translated peptide).
+ * Sets the value of the pos1 property.
*
- * <p>Java class for anonymous complex type</p>.
+ * @param value
+ * allowed object is {@link BigInteger }
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setPos1(BigInteger value)
+ {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
*
+ * @return possible object is {@link BigInteger }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Alcodon {
-
- @XmlAttribute(name = "pos1")
- protected BigInteger pos1;
- @XmlAttribute(name = "pos2")
- protected BigInteger pos2;
- @XmlAttribute(name = "pos3")
- protected BigInteger pos3;
-
- /**
- * Gets the value of the pos1 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos1() {
- return pos1;
- }
-
- /**
- * Sets the value of the pos1 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos1(BigInteger value) {
- this.pos1 = value;
- }
-
- /**
- * Gets the value of the pos2 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos2() {
- return pos2;
- }
-
- /**
- * Sets the value of the pos2 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos2(BigInteger value) {
- this.pos2 = value;
- }
+ public BigInteger getPos2()
+ {
+ return pos2;
+ }
- /**
- * Gets the value of the pos3 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos3() {
- return pos3;
- }
+ /**
+ * Sets the value of the pos2 property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPos2(BigInteger value)
+ {
+ this.pos2 = value;
+ }
- /**
- * Sets the value of the pos3 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos3(BigInteger value) {
- this.pos3 = value;
- }
+ /**
+ * Gets the value of the pos3 property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPos3()
+ {
+ return pos3;
+ }
+ /**
+ * Sets the value of the pos3 property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPos3(BigInteger value)
+ {
+ this.pos3 = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "annotationElement",
- "label",
- "description",
- "thresholdLine",
- "contactmatrix",
- "property"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "annotationElement", "label", "description", "thresholdLine",
+ "contactmatrix", "property" })
@XmlRootElement(name = "Annotation")
-public class Annotation {
-
- protected List<AnnotationElement> annotationElement;
- @XmlElement(required = true)
+public class Annotation
+{
+
+ protected List<AnnotationElement> annotationElement;
+
+ @XmlElement(required = true)
+ protected String label;
+
+ protected String description;
+
+ protected Annotation.ThresholdLine thresholdLine;
+
+ protected List<MapOnAMatrixType> contactmatrix;
+
+ protected List<Property> property;
+
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+
+ /**
+ * height in pixels for the graph if this is a graph-type annotation.
+ *
+ */
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+
+ @XmlAttribute(name = "score")
+ protected Double score;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+
+ /**
+ * is an autocalculated annotation row
+ *
+ */
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+
+ /**
+ * is to be shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ *
+ */
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+
+ /**
+ * Optional string identifier used to group sets of annotation produced by a
+ * particular calculation. Values are opaque strings but have semantic meaning
+ * to Jalview's renderer, data importer and calculation system.
+ *
+ */
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
+
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the annotationElement property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAnnotationElement().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ * </p>
+ *
+ *
+ * @return The value of the annotationElement property.
+ */
+ public List<AnnotationElement> getAnnotationElement()
+ {
+ if (annotationElement == null)
+ {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLabel(String value)
+ {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the thresholdLine property.
+ *
+ * @return possible object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine getThresholdLine()
+ {
+ return thresholdLine;
+ }
+
+ /**
+ * Sets the value of the thresholdLine property.
+ *
+ * @param value
+ * allowed object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value)
+ {
+ this.thresholdLine = value;
+ }
+
+ /**
+ * Gets the value of the contactmatrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the contactmatrix property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getContactmatrix().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapOnAMatrixType }
+ * </p>
+ *
+ *
+ * @return The value of the contactmatrix property.
+ */
+ public List<MapOnAMatrixType> getContactmatrix()
+ {
+ if (contactmatrix == null)
+ {
+ contactmatrix = new ArrayList<MapOnAMatrixType>();
+ }
+ return this.contactmatrix;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Property }
+ * </p>
+ *
+ *
+ * @return The value of the property property.
+ */
+ public List<Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph()
+ {
+ return graph;
+ }
+
+ /**
+ * Sets the value of the graph property.
+ *
+ */
+ public void setGraph(boolean value)
+ {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphType()
+ {
+ return graphType;
+ }
+
+ /**
+ * Sets the value of the graphType property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value)
+ {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getGroupRef()
+ {
+ return groupRef;
+ }
+
+ /**
+ * Sets the value of the groupRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setGroupRef(String value)
+ {
+ this.groupRef = value;
+ }
+
+ /**
+ * Gets the value of the graphColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphColour()
+ {
+ return graphColour;
+ }
+
+ /**
+ * Sets the value of the graphColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value)
+ {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphGroup()
+ {
+ return graphGroup;
+ }
+
+ /**
+ * Sets the value of the graphGroup property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value)
+ {
+ this.graphGroup = value;
+ }
+
+ /**
+ * height in pixels for the graph if this is a graph-type annotation.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphHeight()
+ {
+ return graphHeight;
+ }
+
+ /**
+ * Sets the value of the graphHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getGraphHeight()
+ */
+ public void setGraphHeight(Integer value)
+ {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScoreOnly()
+ {
+ if (scoreOnly == null)
+ {
+ return false;
+ }
+ else
+ {
+ return scoreOnly;
+ }
+ }
+
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value)
+ {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return possible object is {@link Double }
+ *
+ */
+ public Double getScore()
+ {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is {@link Double }
+ *
+ */
+ public void setScore(Double value)
+ {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isVisible()
+ {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels()
+ {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value)
+ {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels()
+ {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value)
+ {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels()
+ {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value)
+ {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * is an autocalculated annotation row
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated()
+ {
+ if (autoCalculated == null)
+ {
+ return false;
+ }
+ else
+ {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isAutoCalculated()
+ */
+ public void setAutoCalculated(Boolean value)
+ {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * is to be shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment()
+ {
+ if (belowAlignment == null)
+ {
+ return true;
+ }
+ else
+ {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isBelowAlignment()
+ */
+ public void setBelowAlignment(Boolean value)
+ {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Optional string identifier used to group sets of annotation produced by a
+ * particular calculation. Values are opaque strings but have semantic meaning
+ * to Jalview's renderer, data importer and calculation system.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getCalcId()
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine
+ {
+
+ @XmlAttribute(name = "label")
protected String label;
- protected String description;
- protected Annotation.ThresholdLine thresholdLine;
- protected List<MapOnAMatrixType> contactmatrix;
- protected List<Property> property;
- @XmlAttribute(name = "graph", required = true)
- protected boolean graph;
- @XmlAttribute(name = "graphType")
- protected Integer graphType;
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "groupRef")
- protected String groupRef;
- @XmlAttribute(name = "graphColour")
- protected Integer graphColour;
- @XmlAttribute(name = "graphGroup")
- protected Integer graphGroup;
- /**
- * height in pixels for the graph if this is a
- * graph-type annotation.
- *
- */
- @XmlAttribute(name = "graphHeight")
- protected Integer graphHeight;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "scoreOnly")
- protected Boolean scoreOnly;
- @XmlAttribute(name = "score")
- protected Double score;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "centreColLabels")
- protected Boolean centreColLabels;
- @XmlAttribute(name = "scaleColLabels")
- protected Boolean scaleColLabels;
- @XmlAttribute(name = "showAllColLabels")
- protected Boolean showAllColLabels;
- /**
- * is an autocalculated annotation row
- *
- */
- @XmlAttribute(name = "autoCalculated")
- protected Boolean autoCalculated;
- /**
- * is to be shown below the alignment - introduced
- * in Jalview 2.8 for visualizing T-COFFEE alignment scores
- *
- */
- @XmlAttribute(name = "belowAlignment")
- protected Boolean belowAlignment;
- /**
- * Optional string identifier used to group sets of
- * annotation produced by a particular calculation. Values are opaque
- * strings but have semantic meaning to Jalview's renderer, data
- * importer and calculation system.
- *
- */
- @XmlAttribute(name = "calcId")
- protected String calcId;
-
- /**
- * Gets the value of the annotationElement property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotationElement property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAnnotationElement().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AnnotationElement }
- * </p>
- *
- *
- * @return
- * The value of the annotationElement property.
- */
- public List<AnnotationElement> getAnnotationElement() {
- if (annotationElement == null) {
- annotationElement = new ArrayList<AnnotationElement>();
- }
- return this.annotationElement;
- }
-
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the thresholdLine property.
- *
- * @return
- * possible object is
- * {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine getThresholdLine() {
- return thresholdLine;
- }
-
- /**
- * Sets the value of the thresholdLine property.
- *
- * @param value
- * allowed object is
- * {@link Annotation.ThresholdLine }
- *
- */
- public void setThresholdLine(Annotation.ThresholdLine value) {
- this.thresholdLine = value;
- }
-
- /**
- * Gets the value of the contactmatrix property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the contactmatrix property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getContactmatrix().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapOnAMatrixType }
- * </p>
- *
- *
- * @return
- * The value of the contactmatrix property.
- */
- public List<MapOnAMatrixType> getContactmatrix() {
- if (contactmatrix == null) {
- contactmatrix = new ArrayList<MapOnAMatrixType>();
- }
- return this.contactmatrix;
- }
-
- /**
- * Gets the value of the property property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Property }
- * </p>
- *
- *
- * @return
- * The value of the property property.
- */
- public List<Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the graph property.
- *
- */
- public boolean isGraph() {
- return graph;
- }
-
- /**
- * Sets the value of the graph property.
- *
- */
- public void setGraph(boolean value) {
- this.graph = value;
- }
-
- /**
- * Gets the value of the graphType property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphType() {
- return graphType;
- }
-
- /**
- * Sets the value of the graphType property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphType(Integer value) {
- this.graphType = value;
- }
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the groupRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * Sets the value of the groupRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGroupRef(String value) {
- this.groupRef = value;
- }
-
- /**
- * Gets the value of the graphColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphColour() {
- return graphColour;
- }
-
- /**
- * Sets the value of the graphColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphColour(Integer value) {
- this.graphColour = value;
- }
-
- /**
- * Gets the value of the graphGroup property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphGroup() {
- return graphGroup;
- }
-
- /**
- * Sets the value of the graphGroup property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphGroup(Integer value) {
- this.graphGroup = value;
- }
-
- /**
- * height in pixels for the graph if this is a
- * graph-type annotation.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphHeight() {
- return graphHeight;
- }
-
- /**
- * Sets the value of the graphHeight property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getGraphHeight()
- */
- public void setGraphHeight(Integer value) {
- this.graphHeight = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the scoreOnly property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScoreOnly() {
- if (scoreOnly == null) {
- return false;
- } else {
- return scoreOnly;
- }
- }
-
- /**
- * Sets the value of the scoreOnly property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScoreOnly(Boolean value) {
- this.scoreOnly = value;
- }
- /**
- * Gets the value of the score property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getScore() {
- return score;
- }
+ @XmlAttribute(name = "value")
+ protected Float value;
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is
- * {@link Double }
- *
- */
- public void setScore(Double value) {
- this.score = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
/**
- * Sets the value of the visible property.
+ * Gets the value of the label property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
-
- /**
- * Gets the value of the centreColLabels property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isCentreColLabels() {
- return centreColLabels;
+ public String getLabel()
+ {
+ return label;
}
/**
- * Sets the value of the centreColLabels property.
+ * Sets the value of the label property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColLabels(Boolean value) {
- this.centreColLabels = value;
- }
-
- /**
- * Gets the value of the scaleColLabels property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isScaleColLabels() {
- return scaleColLabels;
+ public void setLabel(String value)
+ {
+ this.label = value;
}
/**
- * Sets the value of the scaleColLabels property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleColLabels(Boolean value) {
- this.scaleColLabels = value;
- }
-
- /**
- * Gets the value of the showAllColLabels property.
+ * @return possible object is {@link Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowAllColLabels() {
- return showAllColLabels;
+ public Float getValue()
+ {
+ return value;
}
/**
- * Sets the value of the showAllColLabels property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAllColLabels(Boolean value) {
- this.showAllColLabels = value;
- }
-
- /**
- * is an autocalculated annotation row
+ * allowed object is {@link Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isAutoCalculated() {
- if (autoCalculated == null) {
- return false;
- } else {
- return autoCalculated;
- }
+ public void setValue(Float value)
+ {
+ this.value = value;
}
/**
- * Sets the value of the autoCalculated property.
+ * Gets the value of the colour property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isAutoCalculated()
- */
- public void setAutoCalculated(Boolean value) {
- this.autoCalculated = value;
- }
-
- /**
- * is to be shown below the alignment - introduced
- * in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isBelowAlignment() {
- if (belowAlignment == null) {
- return true;
- } else {
- return belowAlignment;
- }
+ public Integer getColour()
+ {
+ return colour;
}
/**
- * Sets the value of the belowAlignment property.
+ * Sets the value of the colour property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isBelowAlignment()
- */
- public void setBelowAlignment(Boolean value) {
- this.belowAlignment = value;
- }
-
- /**
- * Optional string identifier used to group sets of
- * annotation produced by a particular calculation. Values are opaque
- * strings but have semantic meaning to Jalview's renderer, data
- * importer and calculation system.
+ * allowed object is {@link Integer }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getCalcId() {
- return calcId;
+ public void setColour(Integer value)
+ {
+ this.colour = value;
}
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getCalcId()
- */
- public void setCalcId(String value) {
- this.calcId = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class ThresholdLine {
-
- @XmlAttribute(name = "label")
- protected String label;
- @XmlAttribute(name = "value")
- protected Float value;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
-
- }
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for AnnotationColourScheme complex type</p>.
+ * <p>
+ * Java class for AnnotationColourScheme complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="AnnotationColourScheme">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme {
-
- @XmlAttribute(name = "aboveThreshold")
- protected Integer aboveThreshold;
- @XmlAttribute(name = "annotation")
- protected String annotation;
- @XmlAttribute(name = "minColour")
- protected Integer minColour;
- @XmlAttribute(name = "maxColour")
- protected Integer maxColour;
- @XmlAttribute(name = "colourScheme")
- protected String colourScheme;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "perSequence")
- protected Boolean perSequence;
- @XmlAttribute(name = "predefinedColours")
- protected Boolean predefinedColours;
-
- /**
- * Gets the value of the aboveThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getAboveThreshold() {
- return aboveThreshold;
- }
-
- /**
- * Sets the value of the aboveThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setAboveThreshold(Integer value) {
- this.aboveThreshold = value;
- }
-
- /**
- * Gets the value of the annotation property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotation() {
- return annotation;
- }
-
- /**
- * Sets the value of the annotation property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotation(String value) {
- this.annotation = value;
- }
-
- /**
- * Gets the value of the minColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMinColour() {
- return minColour;
- }
-
- /**
- * Sets the value of the minColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMinColour(Integer value) {
- this.minColour = value;
- }
-
- /**
- * Gets the value of the maxColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMaxColour() {
- return maxColour;
- }
-
- /**
- * Sets the value of the maxColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMaxColour(Integer value) {
- this.maxColour = value;
- }
-
- /**
- * Gets the value of the colourScheme property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColourScheme() {
- return colourScheme;
- }
-
- /**
- * Sets the value of the colourScheme property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColourScheme(String value) {
- this.colourScheme = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the perSequence property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPerSequence() {
- return perSequence;
- }
-
- /**
- * Sets the value of the perSequence property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPerSequence(Boolean value) {
- this.perSequence = value;
- }
-
- /**
- * Gets the value of the predefinedColours property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPredefinedColours() {
- return predefinedColours;
- }
-
- /**
- * Sets the value of the predefinedColours property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPredefinedColours(Boolean value) {
- this.predefinedColours = value;
- }
+public class AnnotationColourScheme
+{
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold()
+ {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value)
+ {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAnnotation()
+ {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAnnotation(String value)
+ {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMinColour()
+ {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value)
+ {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMaxColour()
+ {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value)
+ {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColourScheme()
+ {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColourScheme(String value)
+ {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence()
+ {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value)
+ {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value)
+ {
+ this.predefinedColours = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "displayCharacter",
- "description",
- "secondaryStructure",
- "value"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "displayCharacter", "description", "secondaryStructure", "value" })
@XmlRootElement(name = "annotationElement")
-public class AnnotationElement {
-
- protected String displayCharacter;
- protected String description;
- protected String secondaryStructure;
- protected Float value;
- @XmlAttribute(name = "position", required = true)
- protected int position;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the displayCharacter property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDisplayCharacter() {
- return displayCharacter;
- }
-
- /**
- * Sets the value of the displayCharacter property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDisplayCharacter(String value) {
- this.displayCharacter = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSecondaryStructure() {
- return secondaryStructure;
- }
-
- /**
- * Sets the value of the secondaryStructure property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSecondaryStructure(String value) {
- this.secondaryStructure = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- */
- public int getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- */
- public void setPosition(int value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+public class AnnotationElement
+{
+
+ protected String displayCharacter;
+
+ protected String description;
+
+ protected String secondaryStructure;
+
+ protected Float value;
+
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDisplayCharacter()
+ {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value)
+ {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSecondaryStructure()
+ {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value)
+ {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setValue(Float value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value)
+ {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for DoubleMatrix complex type</p>.
+ * <p>
+ * Java class for DoubleMatrix complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="DoubleMatrix">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
- "row",
- "d",
- "e"
-})
-public class DoubleMatrix {
-
- protected List<DoubleVector> row;
- @XmlElement(name = "D")
- protected DoubleVector d;
- @XmlElement(name = "E")
- protected DoubleVector e;
- @XmlAttribute(name = "rows")
- protected Integer rows;
- @XmlAttribute(name = "columns")
- protected Integer columns;
-
- /**
- * Gets the value of the row property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the row property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getRow().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DoubleVector }
- * </p>
- *
- *
- * @return
- * The value of the row property.
- */
- public List<DoubleVector> getRow() {
- if (row == null) {
- row = new ArrayList<DoubleVector>();
- }
- return this.row;
- }
-
- /**
- * Gets the value of the d property.
- *
- * @return
- * possible object is
- * {@link DoubleVector }
- *
- */
- public DoubleVector getD() {
- return d;
- }
-
- /**
- * Sets the value of the d property.
- *
- * @param value
- * allowed object is
- * {@link DoubleVector }
- *
- */
- public void setD(DoubleVector value) {
- this.d = value;
- }
-
- /**
- * Gets the value of the e property.
- *
- * @return
- * possible object is
- * {@link DoubleVector }
- *
- */
- public DoubleVector getE() {
- return e;
- }
-
- /**
- * Sets the value of the e property.
- *
- * @param value
- * allowed object is
- * {@link DoubleVector }
- *
- */
- public void setE(DoubleVector value) {
- this.e = value;
- }
-
- /**
- * Gets the value of the rows property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getRows() {
- return rows;
- }
-
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setRows(Integer value) {
- this.rows = value;
- }
-
- /**
- * Gets the value of the columns property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColumns() {
- return columns;
- }
-
- /**
- * Sets the value of the columns property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColumns(Integer value) {
- this.columns = value;
+@XmlType(
+ name = "DoubleMatrix",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "row", "d", "e" })
+public class DoubleMatrix
+{
+
+ protected List<DoubleVector> row;
+
+ @XmlElement(name = "D")
+ protected DoubleVector d;
+
+ @XmlElement(name = "E")
+ protected DoubleVector e;
+
+ @XmlAttribute(name = "rows")
+ protected Integer rows;
+
+ @XmlAttribute(name = "columns")
+ protected Integer columns;
+
+ /**
+ * Gets the value of the row property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the row property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getRow().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DoubleVector }
+ * </p>
+ *
+ *
+ * @return The value of the row property.
+ */
+ public List<DoubleVector> getRow()
+ {
+ if (row == null)
+ {
+ row = new ArrayList<DoubleVector>();
}
+ return this.row;
+ }
+
+ /**
+ * Gets the value of the d property.
+ *
+ * @return possible object is {@link DoubleVector }
+ *
+ */
+ public DoubleVector getD()
+ {
+ return d;
+ }
+
+ /**
+ * Sets the value of the d property.
+ *
+ * @param value
+ * allowed object is {@link DoubleVector }
+ *
+ */
+ public void setD(DoubleVector value)
+ {
+ this.d = value;
+ }
+
+ /**
+ * Gets the value of the e property.
+ *
+ * @return possible object is {@link DoubleVector }
+ *
+ */
+ public DoubleVector getE()
+ {
+ return e;
+ }
+
+ /**
+ * Sets the value of the e property.
+ *
+ * @param value
+ * allowed object is {@link DoubleVector }
+ *
+ */
+ public void setE(DoubleVector value)
+ {
+ this.e = value;
+ }
+
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getRows()
+ {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setRows(Integer value)
+ {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the columns property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColumns()
+ {
+ return columns;
+ }
+
+ /**
+ * Sets the value of the columns property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColumns(Integer value)
+ {
+ this.columns = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for DoubleVector complex type</p>.
+ * <p>
+ * Java class for DoubleVector complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="DoubleVector">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
- "v"
-})
-public class DoubleVector {
+@XmlType(
+ name = "DoubleVector",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "v" })
+public class DoubleVector
+{
- @XmlElement(type = Double.class)
- protected List<Double> v;
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
- /**
- * Gets the value of the v property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the v property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getV().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Double }
- * </p>
- *
- *
- * @return
- * The value of the v property.
- */
- public List<Double> getV() {
- if (v == null) {
- v = new ArrayList<Double>();
- }
- return this.v;
+ /**
+ * Gets the value of the v property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the v property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getV().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Double }
+ * </p>
+ *
+ *
+ * @return The value of the v property.
+ */
+ public List<Double> getV()
+ {
+ if (v == null)
+ {
+ v = new ArrayList<Double>();
}
+ return this.v;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for feature complex type</p>.
+ * <p>
+ * Java class for feature complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="feature">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
- "otherData"
-})
-public class Feature {
-
- protected List<Feature.OtherData> otherData;
- @XmlAttribute(name = "begin", required = true)
- protected int begin;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "featureGroup")
- protected String featureGroup;
- @XmlAttribute(name = "score")
- protected Float score;
-
- /**
- * Gets the value of the otherData property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the otherData property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getOtherData().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature.OtherData }
- * </p>
- *
- *
- * @return
- * The value of the otherData property.
- */
- public List<Feature.OtherData> getOtherData() {
- if (otherData == null) {
- otherData = new ArrayList<Feature.OtherData>();
- }
- return this.otherData;
+@XmlType(
+ name = "feature",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "otherData" })
+public class Feature
+{
+
+ protected List<Feature.OtherData> otherData;
+
+ @XmlAttribute(name = "begin", required = true)
+ protected int begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ @XmlAttribute(name = "status")
+ protected String status;
+
+ @XmlAttribute(name = "featureGroup")
+ protected String featureGroup;
+
+ @XmlAttribute(name = "score")
+ protected Float score;
+
+ /**
+ * Gets the value of the otherData property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the otherData property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getOtherData().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature.OtherData }
+ * </p>
+ *
+ *
+ * @return The value of the otherData property.
+ */
+ public List<Feature.OtherData> getOtherData()
+ {
+ if (otherData == null)
+ {
+ otherData = new ArrayList<Feature.OtherData>();
}
+ return this.otherData;
+ }
+
+ /**
+ * Gets the value of the begin property.
+ *
+ */
+ public int getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ */
+ public void setBegin(int value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the featureGroup property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFeatureGroup()
+ {
+ return featureGroup;
+ }
+
+ /**
+ * Sets the value of the featureGroup property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFeatureGroup(String value)
+ {
+ this.featureGroup = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScore()
+ {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setScore(Float value)
+ {
+ this.score = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData
+ {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
/**
- * Gets the value of the begin property.
+ * key2 may be used for a sub-attribute of key
*
*/
- public int getBegin() {
- return begin;
- }
+ @XmlAttribute(name = "key2")
+ protected String key2;
- /**
- * Sets the value of the begin property.
- *
- */
- public void setBegin(int value) {
- this.begin = value;
- }
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the end property.
+ * Gets the value of the key property.
*
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
+ * @return possible object is {@link String }
*
*/
- public void setEnd(int value) {
- this.end = value;
+ public String getKey()
+ {
+ return key;
}
/**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the description property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDescription() {
- return description;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the description property.
+ * key2 may be used for a sub-attribute of key
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the status property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getStatus() {
- return status;
+ public String getKey2()
+ {
+ return key2;
}
/**
- * Sets the value of the status property.
+ * Sets the value of the key2 property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the featureGroup property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @see #getKey2()
*/
- public String getFeatureGroup() {
- return featureGroup;
+ public void setKey2(String value)
+ {
+ this.key2 = value;
}
/**
- * Sets the value of the featureGroup property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFeatureGroup(String value) {
- this.featureGroup = value;
- }
-
- /**
- * Gets the value of the score property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getScore() {
- return score;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the score property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScore(Float value) {
- this.score = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class OtherData {
-
- @XmlAttribute(name = "key", required = true)
- protected String key;
- /**
- * key2 may be used for a sub-attribute of key
- *
- */
- @XmlAttribute(name = "key2")
- protected String key2;
- @XmlAttribute(name = "value", required = true)
- protected String value;
-
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
- }
-
- /**
- * key2 may be used for a sub-attribute of key
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey2() {
- return key2;
- }
-
- /**
- * Sets the value of the key2 property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getKey2()
- */
- public void setKey2(String value) {
- this.key2 = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for FeatureMatcher complex type</p>.
+ * <p>
+ * Java class for FeatureMatcher complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="FeatureMatcher">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
- "attributeName",
- "condition",
- "value"
-})
-public class FeatureMatcher {
+@XmlType(
+ name = "FeatureMatcher",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "attributeName", "condition", "value" })
+public class FeatureMatcher
+{
- /**
- * name of feature attribute to filter on, or attribute and sub-attribute
- *
- */
- @XmlElement(namespace = "")
- protected List<String> attributeName;
- @XmlElement(namespace = "", required = true)
- protected String condition;
- @XmlElement(namespace = "", required = true)
- protected String value;
- @XmlAttribute(name = "by")
- protected FilterBy by;
+ /**
+ * name of feature attribute to filter on, or attribute and sub-attribute
+ *
+ */
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
- /**
- * name of feature attribute to filter on, or attribute and sub-attribute
- *
- * Gets the value of the attributeName property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the attributeName property.
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
- /**
- * Gets the value of the condition property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCondition() {
- return condition;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String value;
- /**
- * Sets the value of the condition property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCondition(String value) {
- this.condition = value;
- }
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
+ /**
+ * name of feature attribute to filter on, or attribute and sub-attribute
+ *
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the attributeName property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the attributeName property.
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
}
+ return this.attributeName;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Gets the value of the condition property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCondition()
+ {
+ return condition;
+ }
- /**
- * Gets the value of the by property.
- *
- * @return
- * possible object is
- * {@link FilterBy }
- *
- */
- public FilterBy getBy() {
- return by;
- }
+ /**
+ * Sets the value of the condition property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCondition(String value)
+ {
+ this.condition = value;
+ }
- /**
- * Sets the value of the by property.
- *
- * @param value
- * allowed object is
- * {@link FilterBy }
- *
- */
- public void setBy(FilterBy value) {
- this.by = value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the by property.
+ *
+ * @return possible object is {@link FilterBy }
+ *
+ */
+ public FilterBy getBy()
+ {
+ return by;
+ }
+
+ /**
+ * Sets the value of the by property.
+ *
+ * @param value
+ * allowed object is {@link FilterBy }
+ *
+ */
+ public void setBy(FilterBy value)
+ {
+ this.by = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* A feature match condition, which may be simple or compound
*
- * <p>Java class for FeatureMatcherSet complex type</p>.
+ * <p>
+ * Java class for FeatureMatcherSet complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="FeatureMatcherSet">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
- "matchCondition",
- "compoundMatcher"
-})
-public class FeatureMatcherSet {
-
- @XmlElement(namespace = "")
- protected FeatureMatcher matchCondition;
- @XmlElement(namespace = "")
- protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+@XmlType(
+ name = "FeatureMatcherSet",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "matchCondition", "compoundMatcher" })
+public class FeatureMatcherSet
+{
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcher matchCondition;
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+
+ /**
+ * Gets the value of the matchCondition property.
+ *
+ * @return possible object is {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher getMatchCondition()
+ {
+ return matchCondition;
+ }
+
+ /**
+ * Sets the value of the matchCondition property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcher }
+ *
+ */
+ public void setMatchCondition(FeatureMatcher value)
+ {
+ this.matchCondition = value;
+ }
+
+ /**
+ * Gets the value of the compoundMatcher property.
+ *
+ * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
+ {
+ return compoundMatcher;
+ }
+
+ /**
+ * Sets the value of the compoundMatcher property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
+ {
+ this.compoundMatcher = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ * </sequence>
+ * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "matcherSet" })
+ public static class CompoundMatcher
+ {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
/**
- * Gets the value of the matchCondition property.
+ * If true, matchers are AND-ed, if false they are OR-ed
*
- * @return
- * possible object is
- * {@link FeatureMatcher }
- *
*/
- public FeatureMatcher getMatchCondition() {
- return matchCondition;
- }
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
/**
- * Sets the value of the matchCondition property.
+ * Gets the value of the matcherSet property.
*
- * @param value
- * allowed object is
- * {@link FeatureMatcher }
- *
- */
- public void setMatchCondition(FeatureMatcher value) {
- this.matchCondition = value;
- }
-
- /**
- * Gets the value of the compoundMatcher property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the matcherSet property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getMatcherSet().add(newItem);
+ * </pre>
*
- * @return
- * possible object is
- * {@link FeatureMatcherSet.CompoundMatcher }
- *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureMatcherSet }
+ * </p>
+ *
+ *
+ * @return The value of the matcherSet property.
*/
- public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
- return compoundMatcher;
+ public List<FeatureMatcherSet> getMatcherSet()
+ {
+ if (matcherSet == null)
+ {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
}
/**
- * Sets the value of the compoundMatcher property.
+ * If true, matchers are AND-ed, if false they are OR-ed
*
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet.CompoundMatcher }
- *
*/
- public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
- this.compoundMatcher = value;
+ public boolean isAnd()
+ {
+ return and;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- * </sequence>
- * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * Sets the value of the and property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "matcherSet"
- })
- public static class CompoundMatcher {
-
- @XmlElement(namespace = "", required = true)
- protected List<FeatureMatcherSet> matcherSet;
- /**
- * If true, matchers are AND-ed, if false they are OR-ed
- *
- */
- @XmlAttribute(name = "and", required = true)
- protected boolean and;
-
- /**
- * Gets the value of the matcherSet property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matcherSet property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getMatcherSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link FeatureMatcherSet }
- * </p>
- *
- *
- * @return
- * The value of the matcherSet property.
- */
- public List<FeatureMatcherSet> getMatcherSet() {
- if (matcherSet == null) {
- matcherSet = new ArrayList<FeatureMatcherSet>();
- }
- return this.matcherSet;
- }
-
- /**
- * If true, matchers are AND-ed, if false they are OR-ed
- *
- */
- public boolean isAnd() {
- return and;
- }
-
- /**
- * Sets the value of the and property.
- *
- */
- public void setAnd(boolean value) {
- this.and = value;
- }
-
+ public void setAnd(boolean value)
+ {
+ this.and = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
-
/**
* Filter may apply to label, score or some feature attribute
*
- * <p>Java class for FilterBy</p>.
+ * <p>
+ * Java class for FilterBy
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
* <pre>
* <simpleType name="FilterBy">
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum FilterBy {
+public enum FilterBy
+{
- @XmlEnumValue("byLabel")
- BY_LABEL("byLabel"),
- @XmlEnumValue("byScore")
- BY_SCORE("byScore"),
- @XmlEnumValue("byAttribute")
- BY_ATTRIBUTE("byAttribute");
- private final String value;
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+ BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
- FilterBy(String v) {
- value = v;
- }
+ private final String value;
- /**
- * Gets the value associated to the enum constant.
- *
- * @return
- * The value linked to the enum.
- */
- public String value() {
- return value;
- }
+ FilterBy(String v)
+ {
+ value = v;
+ }
+
+ /**
+ * Gets the value associated to the enum constant.
+ *
+ * @return The value linked to the enum.
+ */
+ public String value()
+ {
+ return value;
+ }
- /**
- * Gets the enum associated to the value passed as parameter.
- *
- * @param v
- * The value to get the enum from.
- * @return
- * The enum which corresponds to the value, if it exists.
- * @throws IllegalArgumentException
- * If no value matches in the enum declaration.
- */
- public static FilterBy fromValue(String v) {
- for (FilterBy c: FilterBy.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+ /**
+ * Gets the enum associated to the value passed as parameter.
+ *
+ * @param v
+ * The value to get the enum from.
+ * @return The enum which corresponds to the value, if it exists.
+ * @throws IllegalArgumentException
+ * If no value matches in the enum declaration.
+ */
+ public static FilterBy fromValue(String v)
+ {
+ for (FilterBy c : FilterBy.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for JalviewModel complex type</p>.
+ * <p>
+ * Java class for JalviewModel complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="JalviewModel">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
- "creationDate",
- "version",
- "vamsasModel",
- "jSeq",
- "jGroup",
- "viewport",
- "userColours",
- "tree",
- "pcaViewer",
- "featureSettings"
-})
-public class JalviewModel {
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
- @XmlElement(required = true)
- protected String version;
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
- @XmlElement(name = "JSeq")
- protected List<JalviewModel.JSeq> jSeq;
- @XmlElement(name = "JGroup")
- protected List<JalviewModel.JGroup> jGroup;
- @XmlElement(name = "Viewport")
- protected List<JalviewModel.Viewport> viewport;
- @XmlElement(name = "UserColours")
- protected List<JalviewModel.UserColours> userColours;
- protected List<JalviewModel.Tree> tree;
- @XmlElement(name = "PcaViewer")
- protected List<JalviewModel.PcaViewer> pcaViewer;
- @XmlElement(name = "FeatureSettings")
- protected JalviewModel.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate() {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setCreationDate(XMLGregorianCalendar value) {
- this.creationDate = value;
+@XmlType(
+ name = "JalviewModel",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+ "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+
+ @XmlElement(required = true)
+ protected String version;
+
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+
+ protected List<JalviewModel.Tree> tree;
+
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate()
+ {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value)
+ {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return possible object is {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel()
+ {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value)
+ {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jSeq property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ * </p>
+ *
+ *
+ * @return The value of the jSeq property.
+ */
+ public List<JalviewModel.JSeq> getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
}
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jGroup property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ * </p>
+ *
+ *
+ * @return The value of the jGroup property.
+ */
+ public List<JalviewModel.JGroup> getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
}
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the viewport property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ * </p>
+ *
+ *
+ * @return The value of the viewport property.
+ */
+ public List<JalviewModel.Viewport> getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList<JalviewModel.Viewport>();
}
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return
- * possible object is
- * {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the userColours property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ * </p>
+ *
+ *
+ * @return The value of the userColours property.
+ */
+ public List<JalviewModel.UserColours> getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList<JalviewModel.UserColours>();
}
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is
- * {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the tree property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ * </p>
+ *
+ *
+ * @return The value of the tree property.
+ */
+ public List<JalviewModel.Tree> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the pcaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the pcaViewer property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ * </p>
+ *
+ *
+ * @return The value of the pcaViewer property.
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer()
+ {
+ if (pcaViewer == null)
+ {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
}
+ return this.pcaViewer;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return possible object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings getFeatureSettings()
+ {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value)
+ {
+ this.featureSettings = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
/**
- * Gets the value of the jSeq property.
+ * Gets the value of the setting property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.</p>
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the setting property.
+ * </p>
*
* <p>
* For example, to add a new item, do as follows:
* </p>
+ *
* <pre>
- * getJSeq().add(newItem);
+ * getSetting().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ * {@link JalviewModel.FeatureSettings.Setting }
* </p>
*
*
- * @return
- * The value of the jSeq property.
+ * @return The value of the setting property.
*/
- public List<JalviewModel.JSeq> getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
+ public List<JalviewModel.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
}
/**
- * Gets the value of the jGroup property.
+ * Gets the value of the group property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.</p>
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the group property.
+ * </p>
*
* <p>
* For example, to add a new item, do as follows:
* </p>
+ *
* <pre>
- * getJGroup().add(newItem);
+ * getGroup().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
+ * {@link JalviewModel.FeatureSettings.Group }
* </p>
*
*
- * @return
- * The value of the jGroup property.
+ * @return The value of the group property.
*/
- public List<JalviewModel.JGroup> getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
+ public List<JalviewModel.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
}
/**
- * Gets the value of the viewport property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.</p>
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
* </p>
+ *
* <pre>
- * getViewport().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
+ * The following schema fragment specifies the expected content contained
+ * within this class.
* </p>
*
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
*
- * @return
- * The value of the viewport property.
*/
- public List<JalviewModel.Viewport> getViewport() {
- if (viewport == null) {
- viewport = new ArrayList<JalviewModel.Viewport>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ /**
+ * name of feature attribute to colour by, or attribute and sub-attribute
+ *
+ */
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+
+ /**
+ * optional filter(s) applied to the feature type
+ *
+ */
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ @XmlAttribute(name = "order")
+ protected Float order;
+
+ /**
+ * Optional minimum colour for graduated feature colour
+ *
+ */
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ /**
+ * threshold value for graduated feature colour
+ *
+ */
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ /**
+ * threshold type for graduated feature colour
+ *
+ */
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * name of feature attribute to colour by, or attribute and sub-attribute
+ *
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String
+ * }
+ * </p>
+ *
+ *
+ * @return The value of the attributeName property.
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * optional filter(s) applied to the feature type
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ * @see #getMatcherSet()
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getOrder()
+ {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setOrder(Float value)
+ {
+ this.order = value;
+ }
+
+ /**
+ * Optional minimum colour for graduated feature colour
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMincolour()
+ {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getMincolour()
+ */
+ public void setMincolour(Integer value)
+ {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
}
- return this.viewport;
+ else
+ {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * threshold value for graduated feature colour
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ * @see #getThreshold()
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * threshold type for graduated feature colour
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getThreshstate()
+ {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getThreshstate()
+ */
+ public void setThreshstate(Integer value)
+ {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}conservationShading"/>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "seq", "annotationColours", "secStrProvider" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
+ protected List<String> secStrProvider;
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "colour")
+ protected String colour;
+
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
/**
- * Gets the value of the userColours property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.</p>
+ * Optional sequence group ID (only needs to be unique for this alignment)
*
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getUserColours().add(newItem);
- * </pre>
+ */
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+
+ /**
+ * Conservation shading increment
*
+ */
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+
+ /**
+ * Percent Identity Threshold
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
- * </p>
+ */
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ /**
+ * Secondary structure consensus shading - since 2.11.4
*
+ */
+ @XmlAttribute(name = "secstrSelected")
+ protected Boolean secstrSelected;
+
+ /**
+ * Secondary structure consensus increment
*
- * @return
- * The value of the userColours property.
*/
- public List<JalviewModel.UserColours> getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
- }
+ @XmlAttribute(name = "secstrThreshold")
+ protected Integer secstrThreshold;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
/**
- * Gets the value of the tree property.
+ * Gets the value of the seq property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.</p>
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the seq property.
+ * </p>
*
* <p>
* For example, to add a new item, do as follows:
* </p>
+ *
* <pre>
- * getTree().add(newItem);
+ * getSeq().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
+ * Objects of the following type(s) are allowed in the list {@link String }
* </p>
*
*
- * @return
- * The value of the tree property.
+ * @return The value of the seq property.
*/
- public List<JalviewModel.Tree> getTree() {
- if (tree == null) {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
+ }
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
}
/**
- * Gets the value of the pcaViewer property.
+ * Gets the value of the secStrProvider property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.</p>
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secStrProvider property.
+ * </p>
*
* <p>
* For example, to add a new item, do as follows:
* </p>
+ *
* <pre>
- * getPcaViewer().add(newItem);
+ * getSecStrProvider().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
+ * Objects of the following type(s) are allowed in the list {@link String }
* </p>
*
*
- * @return
- * The value of the pcaViewer property.
+ * @return The value of the secStrProvider property.
*/
- public List<JalviewModel.PcaViewer> getPcaViewer() {
- if (pcaViewer == null) {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
+ public List<String> getSecStrProvider()
+ {
+ if (secStrProvider == null)
+ {
+ secStrProvider = new ArrayList<String>();
+ }
+ return this.secStrProvider;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link JalviewModel.FeatureSettings }
- *
*/
- public JalviewModel.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public Integer getStart()
+ {
+ return start;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the start property.
*
* @param value
- * allowed object is
- * {@link JalviewModel.FeatureSettings }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setFeatureSettings(JalviewModel.FeatureSettings value) {
- this.featureSettings = value;
+ public void setStart(Integer value)
+ {
+ this.start = value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * Gets the value of the end property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @return possible object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Setting> setting;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Group> group;
-
- /**
- * Gets the value of the setting property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSetting().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Setting }
- * </p>
- *
- *
- * @return
- * The value of the setting property.
- */
- public List<JalviewModel.FeatureSettings.Setting> getSetting() {
- if (setting == null) {
- setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
- }
- return this.setting;
- }
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- /**
- * Gets the value of the group property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Group }
- * </p>
- *
- *
- * @return
- * The value of the group property.
- */
- public List<JalviewModel.FeatureSettings.Group> getGroup() {
- if (group == null) {
- group = new ArrayList<JalviewModel.FeatureSettings.Group>();
- }
- return this.group;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColour()
+ {
+ return colour;
+ }
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColour(String value)
+ {
+ this.colour = value;
+ }
+ /**
+ * Gets the value of the outlineColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName",
- "matcherSet"
- })
- public static class Setting {
-
- /**
- * name of feature attribute to colour by, or attribute and sub-attribute
- *
- */
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
- /**
- * optional filter(s) applied to the feature type
- *
- */
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
- @XmlAttribute(name = "order")
- protected Float order;
- /**
- * Optional minimum colour
- * for graduated
- * feature
- * colour
- *
- */
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- /**
- * threshold value for
- * graduated feature colour
- *
- */
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- /**
- * threshold type for
- * graduated feature colour
- *
- */
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * name of feature attribute to colour by, or attribute and sub-attribute
- *
- * Gets the value of the attributeName property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the attributeName property.
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * optional filter(s) applied to the feature type
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- * @see #getMatcherSet()
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getOrder() {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setOrder(Float value) {
- this.order = value;
- }
-
- /**
- * Optional minimum colour
- * for graduated
- * feature
- * colour
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMincolour() {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getMincolour()
- */
- public void setMincolour(Integer value) {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * threshold value for
- * graduated feature colour
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- * @see #getThreshold()
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * threshold type for
- * graduated feature colour
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getThreshstate() {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getThreshstate()
- */
- public void setThreshstate(Integer value) {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ /**
+ * Sets the value of the outlineColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
+ }
- }
+ /**
+ * Gets the value of the displayBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = value;
}
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText()
+ {
+ return displayText;
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * Sets the value of the displayText property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}conservationShading"/>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
+
+ /**
+ * Gets the value of the colourText property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "seq",
- "annotationColours",
- "secStrProvider"
- })
- public static class JGroup {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
- protected List<String> secStrProvider;
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "colour")
- protected String colour;
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- /**
- * Optional sequence group ID (only
- * needs to be
- * unique for this
- * alignment)
- *
- */
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
- /**
- * Conservation shading increment
- *
- */
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
- /**
- * Percent Identity Threshold
- *
- */
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- /**
- * Secondary structure consensus shading - since 2.11.4
- *
- */
- @XmlAttribute(name = "secstrSelected")
- protected Boolean secstrSelected;
- /**
- * Secondary structure consensus increment
- *
- */
- @XmlAttribute(name = "secstrThreshold")
- protected Integer secstrThreshold;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
+ public Boolean isColourText()
+ {
+ return colourText;
+ }
- /**
- * Gets the value of the seq property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the seq property.
- */
- public List<String> getSeq() {
- if (seq == null) {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
+ /**
+ * Sets the value of the colourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Gets the value of the secStrProvider property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSecStrProvider().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the secStrProvider property.
- */
- public List<String> getSecStrProvider() {
- if (secStrProvider == null) {
- secStrProvider = new ArrayList<String>();
- }
- return this.secStrProvider;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved()
+ {
+ return showUnconserved;
+ }
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Optional sequence group ID (only needs to be unique for this alignment)
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColour() {
- return colour;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getId()
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColour(String value) {
- this.colour = value;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Gets the value of the outlineColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getOutlineColour() {
- return outlineColour;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = value;
+ }
- /**
- * Sets the value of the outlineColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
- }
+ /**
+ * Conservation shading increment
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Gets the value of the displayBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDisplayBoxes() {
- return displayBoxes;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getConsThreshold()
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- /**
- * Sets the value of the displayBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
- /**
- * Gets the value of the displayText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDisplayText() {
- return displayText;
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value)
+ {
+ this.pidSelected = value;
+ }
- /**
- * Sets the value of the displayText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayText(Boolean value) {
- this.displayText = value;
- }
+ /**
+ * Percent Identity Threshold
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Gets the value of the colourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourText() {
- return colourText;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getPidThreshold()
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- /**
- * Sets the value of the colourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourText(Boolean value) {
- this.colourText = value;
- }
+ /**
+ * Secondary structure consensus shading - since 2.11.4
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isSecstrSelected()
+ {
+ if (secstrSelected == null)
+ {
+ return false;
+ }
+ else
+ {
+ return secstrSelected;
+ }
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the secstrSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isSecstrSelected()
+ */
+ public void setSecstrSelected(Boolean value)
+ {
+ this.secstrSelected = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Secondary structure consensus increment
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSecstrThreshold()
+ {
+ return secstrThreshold;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Sets the value of the secstrThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getSecstrThreshold()
+ */
+ public void setSecstrThreshold(Integer value)
+ {
+ this.secstrThreshold = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
-
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
-
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
-
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowUnconserved() {
- return showUnconserved;
- }
-
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
-
- /**
- * Optional sequence group ID (only
- * needs to be
- * unique for this
- * alignment)
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getId()
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
-
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
-
- /**
- * Conservation shading increment
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
-
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getConsThreshold()
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
-
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value) {
- this.pidSelected = value;
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Percent Identity Threshold
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getPidThreshold()
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Secondary structure consensus shading - since 2.11.4
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isSecstrSelected() {
- if (secstrSelected == null) {
- return false;
- } else {
- return secstrSelected;
- }
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Sets the value of the secstrSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isSecstrSelected()
- */
- public void setSecstrSelected(Boolean value) {
- this.secstrSelected = value;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Secondary structure consensus increment
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSecstrThreshold() {
- return secstrThreshold;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Sets the value of the secstrThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getSecstrThreshold()
- */
- public void setSecstrThreshold(Integer value) {
- this.secstrThreshold = value;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+ public static class JSeq
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids> pdbids;
+
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed)
+ * is used
+ *
+ */
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the features property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Feature }
+ * </p>
+ *
+ *
+ * @return The value of the features property.
+ */
+ public List<Feature> getFeatures()
+ {
+ if (features == null)
+ {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the pdbids property.
+ * </p>
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getPdbids().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ * </p>
+ *
+ *
+ * @return The value of the pdbids property.
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "features",
- "pdbids",
- "hiddenSequences",
- "rnaViewer"
- })
- public static class JSeq {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids> pdbids;
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
- /**
- * Reference to a viewer showing
- * RNA structure for this sequence.
- * Schema supports one viewer
- * showing multiple annotations for
- * multiple sequences, though
- * currently only one annotation
- * for one sequence (gapped or
- * trimmed) is used
- *
- */
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
- @XmlAttribute(name = "colour")
- protected Integer colour;
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature }
- * </p>
- *
- *
- * @return
- * The value of the features property.
- */
- public List<Feature> getFeatures() {
- if (features == null) {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
+ public List<JalviewModel.JSeq.Pdbids> getPdbids()
+ {
+ if (pdbids == null)
+ {
+ pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
- /**
- * Gets the value of the pdbids property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
- * </p>
- *
- *
- * @return
- * The value of the pdbids property.
- */
- public List<JalviewModel.JSeq.Pdbids> getPdbids() {
- if (pdbids == null) {
- pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
- }
- return this.pdbids;
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenSequences property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ * </p>
+ *
+ *
+ * @return The value of the hiddenSequences property.
+ */
+ public List<Integer> getHiddenSequences()
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
+
+ /**
+ * Reference to a viewer showing RNA structure for this sequence. Schema
+ * supports one viewer showing multiple annotations for multiple sequences,
+ * though currently only one annotation for one sequence (gapped or trimmed)
+ * is used
+ *
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the rnaViewer property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ * </p>
+ *
+ *
+ * @return The value of the rnaViewer property.
+ */
+ public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
+ {
+ if (rnaViewer == null)
+ {
+ rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isHidden()
+ {
+ return hidden;
+ }
+
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value)
+ {
+ this.hidden = value;
+ }
+
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isViewreference()
+ {
+ return viewreference;
+ }
+
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value)
+ {
+ this.viewreference = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the structureState property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ * </p>
+ *
+ *
+ * @return The value of the structureState property.
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
+ {
+ if (structureState == null)
+ {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
}
+ return this.structureState;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
/**
- * Gets the value of the hiddenSequences property.
+ * additional identifier which properly disambiguates the structure view
+ * from any other view with the same attributes. This is not an ID,
+ * because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A
+ * structureState element citing the same viewId will appear for each
+ * instance.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.</p>
+ */
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be
+ * included in those used to perform a structure superposition (since
+ * Jalview 2.7).
+ *
+ */
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be
+ * included in those used to colour its associated sequences in this
+ * structureState(since Jalview 2.7).
*
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
+ */
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ /**
+ * Flag set if the structure display is coloured by the Jmol state,
+ * rather than by one or more linked alignment views.
*
+ */
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ /**
+ * An identifier for the viewer type, currently either JMOL or CHIMERA
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- * </p>
+ */
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the value property.
*
+ * @return possible object is {@link String }
*
- * @return
- * The value of the hiddenSequences property.
*/
- public List<Integer> getHiddenSequences() {
- if (hiddenSequences == null) {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
+ public String getValue()
+ {
+ return value;
}
/**
- * Reference to a viewer showing
- * RNA structure for this sequence.
- * Schema supports one viewer
- * showing multiple annotations for
- * multiple sequences, though
- * currently only one annotation
- * for one sequence (gapped or
- * trimmed) is used
- *
- * Gets the value of the rnaViewer property.
+ * Sets the value of the value property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.</p>
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
*
+ * @return possible object is {@link Boolean }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
- * </p>
+ */
+ public Boolean isVisible()
+ {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
- * @return
- * The value of the rnaViewer property.
*/
- public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
- if (rnaViewer == null) {
- rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Gets the value of the colour property.
+ * additional identifier which properly disambiguates the structure view
+ * from any other view with the same attributes. This is not an ID,
+ * because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A
+ * structureState element citing the same viewId will appear for each
+ * instance.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getColour() {
- return colour;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
+ * @see #getViewId()
*/
- public void setColour(Integer value) {
- this.colour = value;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the start property.
+ * Flag set if the alignment panel containing this JSeq should be
+ * included in those used to perform a structure superposition (since
+ * Jalview 2.7).
+ *
+ * @return possible object is {@link Boolean }
*
*/
- public int getStart() {
- return start;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Sets the value of the start property.
+ * Sets the value of the alignwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
*
+ * @see #isAlignwithAlignPanel()
*/
- public void setStart(int value) {
- this.start = value;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the end property.
+ * Flag set if the alignment panel containing this JSeq should be
+ * included in those used to colour its associated sequences in this
+ * structureState(since Jalview 2.7).
+ *
+ * @return possible object is {@link Boolean }
*
*/
- public int getEnd() {
- return end;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the end property.
+ * Sets the value of the colourwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
*
+ * @see #isColourwithAlignPanel()
*/
- public void setEnd(int value) {
- this.end = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the id property.
+ * Flag set if the structure display is coloured by the Jmol state,
+ * rather than by one or more linked alignment views.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the id property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link Boolean }
+ *
+ * @see #isColourByJmol()
*/
- public void setId(String value) {
- this.id = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the hidden property.
+ * An identifier for the viewer type, currently either JMOL or CHIMERA
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isHidden() {
- return hidden;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the hidden property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
+ * @see #getType()
*/
- public void setHidden(Boolean value) {
- this.hidden = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the viewreference property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isViewreference() {
- return viewreference;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the viewreference property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setViewreference(Boolean value) {
- this.viewreference = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * Gets the value of the height property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @return possible object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
+ public void setHeight(Integer value)
{
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- * </p>
- *
- *
- * @return
- * The value of the structureState property.
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
- if (structureState == null) {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
-
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class StructureState {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- /**
- * additional
- * identifier
- * which
- * properly
- * disambiguates
- * the
- * structure
- * view
- * from
- * any
- * other
- * view
- * with
- * the
- * same
- * attributes.
- * This
- * is
- * not
- * an
- * ID,
- * because
- * it
- * is
- * possible
- * to
- * have
- * many
- * references
- * to
- * the
- * same
- * physical
- * structure
- * view
- * from
- * different
- * sequences
- * in
- * an
- * alignment.
- * A
- * structureState
- * element
- * citing
- * the
- * same
- * viewId
- * will
- * appear
- * for
- * each
- * instance.
- *
- */
- @XmlAttribute(name = "viewId")
- protected String viewId;
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- */
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- */
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
- /**
- * Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- */
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
- /**
- * An
- * identifier
- * for
- * the
- * viewer
- * type,
- * currently
- * either
- * JMOL
- * or
- * CHIMERA
- *
- */
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
-
- /**
- * additional
- * identifier
- * which
- * properly
- * disambiguates
- * the
- * structure
- * view
- * from
- * any
- * other
- * view
- * with
- * the
- * same
- * attributes.
- * This
- * is
- * not
- * an
- * ID,
- * because
- * it
- * is
- * possible
- * to
- * have
- * many
- * references
- * to
- * the
- * same
- * physical
- * structure
- * view
- * from
- * different
- * sequences
- * in
- * an
- * alignment.
- * A
- * structureState
- * element
- * citing
- * the
- * same
- * viewId
- * will
- * appear
- * for
- * each
- * instance.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getViewId()
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * perform
- * a
- * structure
- * superposition
- * (since
- * Jalview
- * 2.7).
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel() {
- if (alignwithAlignPanel == null) {
- return true;
- } else {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isAlignwithAlignPanel()
- */
- public void setAlignwithAlignPanel(Boolean value) {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Flag
- * set
- * if
- * the
- * alignment
- * panel
- * containing
- * this
- * JSeq
- * should
- * be
- * included
- * in
- * those
- * used
- * to
- * colour
- * its
- * associated
- * sequences
- * in
- * this
- * structureState(since
- * Jalview
- * 2.7).
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel() {
- if (colourwithAlignPanel == null) {
- return false;
- } else {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isColourwithAlignPanel()
- */
- public void setColourwithAlignPanel(Boolean value) {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Flag
- * set
- * if
- * the
- * structure
- * display
- * is
- * coloured
- * by
- * the
- * Jmol
- * state,
- * rather
- * than
- * by
- * one
- * or
- * more
- * linked
- * alignment
- * views.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourByJmol() {
- if (colourByJmol == null) {
- return true;
- } else {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isColourByJmol()
- */
- public void setColourByJmol(Boolean value) {
- this.colourByJmol = value;
- }
-
- /**
- * An
- * identifier
- * for
- * the
- * viewer
- * type,
- * currently
- * either
- * JMOL
- * or
- * CHIMERA
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getType()
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
- }
-
+ this.height = value;
}
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * Sets the value of the xpos property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @param value
+ * allowed object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
- @XmlAttribute(name = "title")
- protected String title;
- /**
- * An id unique to the RNA
- * viewer panel
- *
- */
- @XmlAttribute(name = "viewId")
- protected String viewId;
- /**
- * horizontal position of
- * split pane divider
- *
- */
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
- /**
- * Index of the selected
- * structure in the viewer
- * panel
- *
- */
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- * </p>
- *
- *
- * @return
- * The value of the secondaryStructure property.
- */
- public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
- if (secondaryStructure == null) {
- secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * An id unique to the RNA
- * viewer panel
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getViewId()
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * horizontal position of
- * split pane divider
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getDividerLocation() {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getDividerLocation()
- */
- public void setDividerLocation(Integer value) {
- this.dividerLocation = value;
- }
-
- /**
- * Index of the selected
- * structure in the viewer
- * panel
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSelectedRna() {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getSelectedRna()
- */
- public void setSelectedRna(Integer value) {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure {
-
- @XmlAttribute(name = "title")
- protected String title;
- /**
- * id attribute
- * of
- * Annotation
- * in
- * vamsasModel
- * for the
- * secondary
- * structure
- * annotation
- * shown in the
- * viewer
- *
- */
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
- /**
- * if true the
- * RNA
- * structure is
- * shown with
- * gaps, if
- * false
- * without
- *
- */
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
- /**
- * name of the
- * project jar
- * entry that
- * holds the
- * VARNA viewer
- * state for
- * the
- * structure
- *
- */
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * id attribute
- * of
- * Annotation
- * in
- * vamsasModel
- * for the
- * secondary
- * structure
- * annotation
- * shown in the
- * viewer
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotationId() {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getAnnotationId()
- */
- public void setAnnotationId(String value) {
- this.annotationId = value;
- }
-
- /**
- * if true the
- * RNA
- * structure is
- * shown with
- * gaps, if
- * false
- * without
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGapped() {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isGapped()
- */
- public void setGapped(Boolean value) {
- this.gapped = value;
- }
-
- /**
- * name of the
- * project jar
- * entry that
- * holds the
- * VARNA viewer
- * state for
- * the
- * structure
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewerState() {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getViewerState()
- */
- public void setViewerState(String value) {
- this.viewerState = value;
- }
-
- }
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
}
- }
+ }
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
+ * <element name="secondaryStructure" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
* </sequence>
* <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
* <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "sequencePoint",
- "axis",
- "seqPointMin",
- "seqPointMax",
- "pcaData"
- })
- public static class PcaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
- /**
- * endpoints of X, Y and Z axes in that order
- *
- */
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.Axis> axis;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected PcaDataType pcaData;
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ /**
+ * An id unique to the RNA viewer panel
+ *
+ */
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ /**
+ * horizontal position of split pane divider
+ *
+ */
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+
+ /**
+ * Index of the selected structure in the viewer panel
+ *
+ */
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secondaryStructure property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ * </p>
+ *
+ *
+ * @return The value of the secondaryStructure property.
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
+ {
+ if (secondaryStructure == null)
+ {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * An id unique to the RNA viewer panel
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getViewId()
+ */
+ public void setViewId(String value)
+ {
+ this.viewId = value;
+ }
+
+ /**
+ * horizontal position of split pane divider
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getDividerLocation()
+ {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getDividerLocation()
+ */
+ public void setDividerLocation(Integer value)
+ {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Index of the selected structure in the viewer panel
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSelectedRna()
+ {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getSelectedRna()
+ */
+ public void setSelectedRna(Integer value)
+ {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
+
@XmlAttribute(name = "title")
protected String title;
- @XmlAttribute(name = "scoreModelName")
- protected String scoreModelName;
- @XmlAttribute(name = "xDim")
- protected Integer xDim;
- @XmlAttribute(name = "yDim")
- protected Integer yDim;
- @XmlAttribute(name = "zDim")
- protected Integer zDim;
- @XmlAttribute(name = "bgColour")
- protected Integer bgColour;
- @XmlAttribute(name = "scaleFactor")
- protected Float scaleFactor;
- @XmlAttribute(name = "showLabels")
- protected Boolean showLabels;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
- @XmlAttribute(name = "includeGaps")
- protected Boolean includeGaps;
- @XmlAttribute(name = "matchGaps")
- protected Boolean matchGaps;
- @XmlAttribute(name = "includeGappedColumns")
- protected Boolean includeGappedColumns;
- @XmlAttribute(name = "denominateByShortestLength")
- protected Boolean denominateByShortestLength;
-
- /**
- * Gets the value of the sequencePoint property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSequencePoint().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.SequencePoint }
- * </p>
- *
- *
- * @return
- * The value of the sequencePoint property.
- */
- public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
- if (sequencePoint == null) {
- sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
- }
- return this.sequencePoint;
- }
-
- /**
- * endpoints of X, Y and Z axes in that order
- *
- * Gets the value of the axis property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the axis property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAxis().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.Axis }
- * </p>
- *
- *
- * @return
- * The value of the axis property.
- */
- public List<JalviewModel.PcaViewer.Axis> getAxis() {
- if (axis == null) {
- axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
- }
- return this.axis;
- }
-
- /**
- * Gets the value of the seqPointMin property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
- return seqPointMin;
- }
-
- /**
- * Sets the value of the seqPointMin property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
- this.seqPointMin = value;
- }
-
- /**
- * Gets the value of the seqPointMax property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
- return seqPointMax;
- }
/**
- * Sets the value of the seqPointMax property.
+ * id attribute of Annotation in vamsasModel for the secondary structure
+ * annotation shown in the viewer
*
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
*/
- public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
- this.seqPointMax = value;
- }
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
/**
- * Gets the value of the pcaData property.
+ * if true the RNA structure is shown with gaps, if false without
*
- * @return
- * possible object is
- * {@link PcaDataType }
- *
*/
- public PcaDataType getPcaData() {
- return pcaData;
- }
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
/**
- * Sets the value of the pcaData property.
+ * name of the project jar entry that holds the VARNA viewer state for
+ * the structure
*
- * @param value
- * allowed object is
- * {@link PcaDataType }
- *
*/
- public void setPcaData(PcaDataType value) {
- this.pcaData = value;
- }
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
/**
* Gets the value of the title property.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScoreModelName() {
- return scoreModelName;
- }
-
- /**
- * Sets the value of the scoreModelName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScoreModelName(String value) {
- this.scoreModelName = value;
- }
-
- /**
- * Gets the value of the xDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXDim() {
- return xDim;
- }
-
- /**
- * Sets the value of the xDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXDim(Integer value) {
- this.xDim = value;
- }
-
- /**
- * Gets the value of the yDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYDim() {
- return yDim;
- }
-
- /**
- * Sets the value of the yDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYDim(Integer value) {
- this.yDim = value;
- }
-
- /**
- * Gets the value of the zDim property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getZDim() {
- return zDim;
+ public String getTitle()
+ {
+ return title;
}
/**
- * Sets the value of the zDim property.
+ * Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setZDim(Integer value) {
- this.zDim = value;
- }
-
- /**
- * Gets the value of the bgColour property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getBgColour() {
- return bgColour;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Sets the value of the bgColour property.
+ * id attribute of Annotation in vamsasModel for the secondary structure
+ * annotation shown in the viewer
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setBgColour(Integer value) {
- this.bgColour = value;
- }
-
- /**
- * Gets the value of the scaleFactor property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getScaleFactor() {
- return scaleFactor;
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the scaleFactor property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScaleFactor(Float value) {
- this.scaleFactor = value;
- }
-
- /**
- * Gets the value of the showLabels property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
+ * @see #getAnnotationId()
*/
- public Boolean isShowLabels() {
- return showLabels;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Sets the value of the showLabels property.
+ * if true the RNA structure is shown with gaps, if false without
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value) {
- this.showLabels = value;
- }
-
- /**
- * Gets the value of the linkToAllViews property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isLinkToAllViews() {
- return linkToAllViews;
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the linkToAllViews property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
-
- /**
- * Gets the value of the width property.
+ * allowed object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
+ * @see #isGapped()
*/
- public Integer getWidth() {
- return width;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Sets the value of the width property.
+ * name of the project jar entry that holds the VARNA viewer state for
+ * the structure
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getHeight() {
- return height;
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
+ * allowed object is {@link String }
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
+ * @see #getViewerState()
*/
- public void setXpos(Integer value) {
- this.xpos = value;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+ public static class PcaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * endpoints of X, Y and Z axes in that order
+ *
+ */
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ @XmlAttribute(name = "title")
+ protected String title;
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
- }
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
- }
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
- }
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
- }
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
- }
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
- }
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
/**
- * <p>Java class for anonymous complex type</p>.
+ * Gets the value of the sequencePoint property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the sequencePoint property.
+ * </p>
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSequencePoint().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ * </p>
+ *
+ *
+ * @return The value of the sequencePoint property.
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
+ {
+ if (sequencePoint == null)
+ {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- /**
- * Set for trees associated with columns of an alignment, sequence or annotation row
- *
- */
- @XmlAttribute(name = "columnWise")
- protected Boolean columnWise;
- /**
- * Refers to annotation row the tree is provided by
- *
- */
- @XmlAttribute(name = "columnReference")
- protected String columnReference;
- /**
- * Tree ID added for binding tree
- * visualization
- * settings to vamsas
- * document trees in jalview 2.4.1
- *
- */
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * endpoints of X, Y and Z axes in that order
+ *
+ * Gets the value of the axis property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the axis property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ * </p>
+ *
+ *
+ * @return The value of the axis property.
+ */
+ public List<JalviewModel.PcaViewer.Axis> getAxis()
+ {
+ if (axis == null)
+ {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+ {
+ return seqPointMin;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
+ {
+ this.seqPointMin = value;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+ {
+ return seqPointMax;
+ }
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNewick(String value) {
- this.newick = value;
- }
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+ {
+ this.seqPointMax = value;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return possible object is {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData()
+ {
+ return pcaData;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value)
+ {
+ this.pcaData = value;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScoreModelName()
+ {
+ return scoreModelName;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Sets the value of the scoreModelName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScoreModelName(String value)
+ {
+ this.scoreModelName = value;
+ }
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXDim()
+ {
+ return xDim;
+ }
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
+ /**
+ * Sets the value of the xDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXDim(Integer value)
+ {
+ this.xDim = value;
+ }
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBootstrap() {
- return showBootstrap;
- }
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYDim()
+ {
+ return yDim;
+ }
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
+ /**
+ * Sets the value of the yDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYDim(Integer value)
+ {
+ this.yDim = value;
+ }
- /**
- * Gets the value of the showDistances property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDistances() {
- return showDistances;
- }
+ /**
+ * Gets the value of the zDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getZDim()
+ {
+ return zDim;
+ }
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
- }
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setZDim(Integer value)
+ {
+ this.zDim = value;
+ }
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value)
+ {
+ this.bgColour = value;
+ }
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScaleFactor()
+ {
+ return scaleFactor;
+ }
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value)
+ {
+ this.scaleFactor = value;
+ }
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels()
+ {
+ return showLabels;
+ }
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value)
+ {
+ this.showLabels = value;
+ }
- /**
- * Set for trees associated with columns of an alignment, sequence or annotation row
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColumnWise() {
- if (columnWise == null) {
- return false;
- } else {
- return columnWise;
- }
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews()
+ {
+ return linkToAllViews;
+ }
- /**
- * Sets the value of the columnWise property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isColumnWise()
- */
- public void setColumnWise(Boolean value) {
- this.columnWise = value;
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
- /**
- * Refers to annotation row the tree is provided by
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColumnReference() {
- return columnReference;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Sets the value of the columnReference property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getColumnReference()
- */
- public void setColumnReference(String value) {
- this.columnReference = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Tree ID added for binding tree
- * visualization
- * settings to vamsas
- * document trees in jalview 2.4.1
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getId()
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isLinkToAllViews() {
- if (linkToAllViews == null) {
- return false;
- } else {
- return linkToAllViews;
- }
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value)
+ {
+ this.includeGaps = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps()
+ {
+ return matchGaps;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value)
+ {
+ this.matchGaps = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns()
+ {
+ return includeGappedColumns;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value)
+ {
+ this.includeGappedColumns = value;
+ }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength()
+ {
+ return denominateByShortestLength;
}
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value)
+ {
+ this.denominateByShortestLength = value;
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attGroup ref="{www.jalview.org}position"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
-
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
+ @XmlType(name = "")
+ public static class Axis
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
}
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="overview" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attGroup ref="{www.jalview.org}conservationShading"/>
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attGroup ref="{www.jalview.org}position"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "annotationColours",
- "hiddenColumns",
- "calcIdParam",
- "overview",
- "secStrProvider"
- })
- public static class Viewport {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
- @XmlElement(namespace = "www.jalview.org")
- protected JalviewModel.Viewport.Overview overview;
- @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
- protected List<String> secStrProvider;
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
- @XmlAttribute(name = "showText")
- protected Boolean showText;
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
- @XmlAttribute(name = "showStructureProviders")
- protected Boolean showStructureProviders;
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
- /**
- * whether a new group has conservation displayed by default
- *
- */
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
- /**
- * whether a new group has consensus displayed by default
- *
- */
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
- /**
- * whether a new group has secondary structure consensus displayed by default
- *
- */
- @XmlAttribute(name = "showGroupSecStrConsensus")
- protected Boolean showGroupSecStrConsensus;
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
- @XmlAttribute(name = "charWidth")
- protected Integer charWidth;
- @XmlAttribute(name = "charHeight")
- protected Integer charHeight;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "idWidth")
- protected Integer idWidth;
- @XmlAttribute(name = "idWidthManuallyAdjusted")
- protected Boolean idWidthManuallyAdjusted;
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
- @XmlAttribute(name = "viewName")
- protected String viewName;
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- /**
- * unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- */
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- /**
- * The viewport id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- */
- @XmlAttribute(name = "complementId")
- protected String complementId;
- @XmlAttribute(name = "showComplementFeatures")
- protected Boolean showComplementFeatures;
- @XmlAttribute(name = "showComplementFeaturesOnTop")
- protected Boolean showComplementFeaturesOnTop;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
- /**
- * Conservation shading increment
- *
- */
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
- /**
- * Percent Identity Threshold
- *
- */
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- /**
- * Secondary structure consensus shading - since 2.11.4
- *
- */
- @XmlAttribute(name = "secstrSelected")
- protected Boolean secstrSelected;
- /**
- * Secondary structure consensus increment
- *
- */
- @XmlAttribute(name = "secstrThreshold")
- protected Integer secstrThreshold;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
+ @XmlType(name = "")
+ public static class SeqPointMin
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint
+ {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the hiddenColumns property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getHiddenColumns().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.HiddenColumns }
- * </p>
- *
- *
- * @return
- * The value of the hiddenColumns property.
- */
- public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
- if (hiddenColumns == null) {
- hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
+ }
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getCalcIdParam().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.CalcIdParam }
- * </p>
- *
- *
- * @return
- * The value of the calcIdParam property.
- */
- public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
- if (calcIdParam == null) {
- calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
- /**
- * Gets the value of the overview property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview getOverview() {
- return overview;
- }
+ /**
+ * Set for trees associated with columns of an alignment, sequence or
+ * annotation row
+ *
+ */
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
- /**
- * Sets the value of the overview property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.Viewport.Overview }
- *
- */
- public void setOverview(JalviewModel.Viewport.Overview value) {
- this.overview = value;
- }
+ /**
+ * Refers to annotation row the tree is provided by
+ *
+ */
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
- /**
- * Gets the value of the secStrProvider property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secStrProvider property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSecStrProvider().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the secStrProvider property.
- */
- public List<String> getSecStrProvider() {
- if (secStrProvider == null) {
- secStrProvider = new ArrayList<String>();
- }
- return this.secStrProvider;
- }
+ /**
+ * Tree ID added for binding tree visualization settings to vamsas document
+ * trees in jalview 2.4.1
+ *
+ */
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBgColour(String value) {
- this.bgColour = value;
- }
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
- /**
- * Gets the value of the showFullId property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowFullId() {
- return showFullId;
- }
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value) {
- this.showFullId = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRightAlignIds() {
- return rightAlignIds;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value) {
- this.rightAlignIds = value;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowText() {
- return showText;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowText(Boolean value) {
- this.showText = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowColourText() {
- return showColourText;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value) {
- this.showColourText = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowUnconserved() {
- if (showUnconserved == null) {
- return false;
- } else {
- return showUnconserved;
- }
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBoxes() {
- return showBoxes;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value) {
- this.showBoxes = value;
- }
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isWrapAlignment() {
- return wrapAlignment;
- }
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value) {
- this.wrapAlignment = value;
- }
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRenderGaps() {
- return renderGaps;
- }
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value) {
- this.renderGaps = value;
- }
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures() {
- return showSequenceFeatures;
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value) {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip() {
- return showNPfeatureTooltip;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
+
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
+
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = value;
+ }
+
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
+
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value)
+ {
+ this.currentTree = value;
+ }
+
+ /**
+ * Set for trees associated with columns of an alignment, sequence or
+ * annotation row
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isColumnWise()
+ {
+ if (columnWise == null)
+ {
+ return false;
+ }
+ else
+ {
+ return columnWise;
+ }
+ }
+
+ /**
+ * Sets the value of the columnWise property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isColumnWise()
+ */
+ public void setColumnWise(Boolean value)
+ {
+ this.columnWise = value;
+ }
+
+ /**
+ * Refers to annotation row the tree is provided by
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColumnReference()
+ {
+ return columnReference;
+ }
+
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getColumnReference()
+ */
+ public void setColumnReference(String value)
+ {
+ this.columnReference = value;
+ }
+
+ /**
+ * Tree ID added for binding tree visualization settings to vamsas document
+ * trees in jalview 2.4.1
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getId()
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews()
+ {
+ if (linkToAllViews == null)
+ {
+ return false;
+ }
+ else
+ {
+ return linkToAllViews;
+ }
+ }
+
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "userColourScheme" })
+ public static class UserColours
+ {
+
+ @XmlElement(
+ name = "UserColourScheme",
+ namespace = "www.jalview.org",
+ required = true)
+ protected JalviewUserColours userColourScheme;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
+ }
+
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attGroup ref="{www.jalview.org}conservationShading"/>
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "annotationColours", "hiddenColumns", "calcIdParam", "overview",
+ "secStrProvider" })
+ public static class Viewport
+ {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
+
+ @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
+ protected List<String> secStrProvider;
+
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
+
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
+
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+
+ @XmlAttribute(name = "showStructureProviders")
+ protected Boolean showStructureProviders;
+
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+
+ /**
+ * whether a new group has conservation displayed by default
+ *
+ */
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+
+ /**
+ * whether a new group has consensus displayed by default
+ *
+ */
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+
+ /**
+ * whether a new group has secondary structure consensus displayed by
+ * default
+ *
+ */
+ @XmlAttribute(name = "showGroupSecStrConsensus")
+ protected Boolean showGroupSecStrConsensus;
+
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
+
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "idWidth")
+ protected Integer idWidth;
+
+ @XmlAttribute(name = "idWidthManuallyAdjusted")
+ protected Boolean idWidthManuallyAdjusted;
+
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ /**
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ */
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ /**
+ * The viewport id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ */
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
+
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+
+ /**
+ * Conservation shading increment
+ *
+ */
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+
+ /**
+ * Percent Identity Threshold
+ *
+ */
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ /**
+ * Secondary structure consensus shading - since 2.11.4
+ *
+ */
+ @XmlAttribute(name = "secstrSelected")
+ protected Boolean secstrSelected;
+
+ /**
+ * Secondary structure consensus increment
+ *
+ */
+ @XmlAttribute(name = "secstrThreshold")
+ protected Integer secstrThreshold;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenColumns property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ * </p>
+ *
+ *
+ * @return The value of the hiddenColumns property.
+ */
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
+ {
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
+
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the calcIdParam property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ * </p>
+ *
+ *
+ * @return The value of the calcIdParam property.
+ */
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
+ {
+ if (calcIdParam == null)
+ {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
+
+ /**
+ * Gets the value of the overview property.
+ *
+ * @return possible object is {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview()
+ {
+ return overview;
+ }
+
+ /**
+ * Sets the value of the overview property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public void setOverview(JalviewModel.Viewport.Overview value)
+ {
+ this.overview = value;
+ }
+
+ /**
+ * Gets the value of the secStrProvider property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secStrProvider property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSecStrProvider().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the secStrProvider property.
+ */
+ public List<String> getSecStrProvider()
+ {
+ if (secStrProvider == null)
+ {
+ secStrProvider = new ArrayList<String>();
+ }
+ return this.secStrProvider;
+ }
+
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBgColour()
+ {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBgColour(String value)
+ {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId()
+ {
+ return showFullId;
+ }
+
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value)
+ {
+ this.showFullId = value;
+ }
+
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value)
+ {
+ this.rightAlignIds = value;
+ }
+
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowText()
+ {
+ return showText;
+ }
+
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value)
+ {
+ this.showText = value;
+ }
+
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value)
+ {
+ this.showColourText = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved()
+ {
+ if (showUnconserved == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showUnconserved;
+ }
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value) {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip() {
- return showDbRefTooltip;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes()
+ {
+ return showBoxes;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value) {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value)
+ {
+ this.showBoxes = value;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowHighlight() {
- if (followHighlight == null) {
- return true;
- } else {
- return followHighlight;
- }
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment()
+ {
+ return wrapAlignment;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value) {
- this.followHighlight = value;
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value)
+ {
+ this.wrapAlignment = value;
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowSelection() {
- if (followSelection == null) {
- return true;
- } else {
- return followSelection;
- }
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value) {
- this.followSelection = value;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value)
+ {
+ this.renderGaps = value;
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value) {
- this.showAnnotation = value;
- }
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Gets the value of the showStructureProviders property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowStructureProviders() {
- return showStructureProviders;
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * Sets the value of the showStructureProviders property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowStructureProviders(Boolean value) {
- this.showStructureProviders = value;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value)
+ {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels() {
- if (centreColumnLabels == null) {
- return false;
- } else {
- return centreColumnLabels;
- }
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value) {
- this.centreColumnLabels = value;
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = value;
+ }
- /**
- * whether a new group has conservation displayed by default
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConservation() {
- if (showGroupConservation == null) {
- return false;
- } else {
- return showGroupConservation;
- }
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isShowGroupConservation()
- */
- public void setShowGroupConservation(Boolean value) {
- this.showGroupConservation = value;
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = value;
+ }
- /**
- * whether a new group has consensus displayed by default
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus() {
- if (showGroupConsensus == null) {
- return false;
- } else {
- return showGroupConsensus;
- }
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isShowGroupConsensus()
- */
- public void setShowGroupConsensus(Boolean value) {
- this.showGroupConsensus = value;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = value;
+ }
- /**
- * whether a new group has secondary structure consensus displayed by default
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupSecStrConsensus() {
- if (showGroupSecStrConsensus == null) {
- return false;
- } else {
- return showGroupSecStrConsensus;
- }
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * Sets the value of the showGroupSecStrConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isShowGroupSecStrConsensus()
- */
- public void setShowGroupSecStrConsensus(Boolean value) {
- this.showGroupSecStrConsensus = value;
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = value;
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * Gets the value of the showStructureProviders property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowStructureProviders()
+ {
+ return showStructureProviders;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = value;
- }
+ /**
+ * Sets the value of the showStructureProviders property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowStructureProviders(Boolean value)
+ {
+ this.showStructureProviders = value;
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = value;
- }
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = value;
+ }
- /**
- * Gets the value of the charWidth property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getCharWidth() {
- return charWidth;
- }
+ /**
+ * whether a new group has conservation displayed by default
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * Sets the value of the charWidth property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setCharWidth(Integer value) {
- this.charWidth = value;
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isShowGroupConservation()
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = value;
+ }
+
+ /**
+ * whether a new group has consensus displayed by default
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Gets the value of the charHeight property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getCharHeight() {
- return charHeight;
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isShowGroupConsensus()
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the charHeight property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setCharHeight(Integer value) {
- this.charHeight = value;
- }
+ /**
+ * whether a new group has secondary structure consensus displayed by
+ * default
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupSecStrConsensus()
+ {
+ if (showGroupSecStrConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupSecStrConsensus;
+ }
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Sets the value of the showGroupSecStrConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isShowGroupSecStrConsensus()
+ */
+ public void setShowGroupSecStrConsensus(Boolean value)
+ {
+ this.showGroupSecStrConsensus = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartRes()
+ {
+ return startRes;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value)
+ {
+ this.startRes = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartSeq()
+ {
+ return startSeq;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value)
+ {
+ this.startSeq = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the charWidth property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharWidth()
+ {
+ return charWidth;
+ }
- /**
- * Gets the value of the idWidth property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getIdWidth() {
- return idWidth;
- }
+ /**
+ * Sets the value of the charWidth property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharWidth(Integer value)
+ {
+ this.charWidth = value;
+ }
- /**
- * Sets the value of the idWidth property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setIdWidth(Integer value) {
- this.idWidth = value;
- }
+ /**
+ * Gets the value of the charHeight property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getCharHeight()
+ {
+ return charHeight;
+ }
- /**
- * Gets the value of the idWidthManuallyAdjusted property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIdWidthManuallyAdjusted() {
- return idWidthManuallyAdjusted;
- }
+ /**
+ * Sets the value of the charHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setCharHeight(Integer value)
+ {
+ this.charHeight = value;
+ }
- /**
- * Sets the value of the idWidthManuallyAdjusted property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIdWidthManuallyAdjusted(Boolean value) {
- this.idWidthManuallyAdjusted = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna() {
- if (scaleProteinAsCdna == null) {
- return true;
- } else {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value) {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewName(String value) {
- this.viewName = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceSetId(String value) {
- this.sequenceSetId = value;
- }
+ /**
+ * Gets the value of the idWidth property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getIdWidth()
+ {
+ return idWidth;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGatheredViews() {
- return gatheredViews;
- }
+ /**
+ * Sets the value of the idWidth property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setIdWidth(Integer value)
+ {
+ this.idWidth = value;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value) {
- this.gatheredViews = value;
- }
+ /**
+ * Gets the value of the idWidthManuallyAdjusted property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIdWidthManuallyAdjusted()
+ {
+ return idWidthManuallyAdjusted;
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the idWidthManuallyAdjusted property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIdWidthManuallyAdjusted(Boolean value)
+ {
+ this.idWidthManuallyAdjusted = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ if (scaleProteinAsCdna == null)
+ {
+ return true;
+ }
+ else
+ {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value)
+ {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewName()
+ {
+ return viewName;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewName(String value)
+ {
+ this.viewName = value;
+ }
+
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceSetId()
+ {
+ return sequenceSetId;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceSetId(String value)
+ {
+ this.sequenceSetId = value;
+ }
- /**
- * unique id used by jalview to
- * synchronize
- * between stored and
- * instantiated views
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews()
+ {
+ return gatheredViews;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getId()
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value)
+ {
+ this.gatheredViews = value;
+ }
- /**
- * The viewport id of this viewport's
- * (cdna/protein) coding complement, if any
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComplementId() {
- return complementId;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getComplementId()
- */
- public void setComplementId(String value) {
- this.complementId = value;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Gets the value of the showComplementFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeatures() {
- if (showComplementFeatures == null) {
- return false;
- } else {
- return showComplementFeatures;
- }
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Sets the value of the showComplementFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeatures(Boolean value) {
- this.showComplementFeatures = value;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Gets the value of the showComplementFeaturesOnTop property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeaturesOnTop() {
- if (showComplementFeaturesOnTop == null) {
- return false;
- } else {
- return showComplementFeaturesOnTop;
- }
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Sets the value of the showComplementFeaturesOnTop property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeaturesOnTop(Boolean value) {
- this.showComplementFeaturesOnTop = value;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * unique id used by jalview to synchronize between stored and instantiated
+ * views
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getId()
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * The viewport id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComplementId()
+ {
+ return complementId;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getComplementId()
+ */
+ public void setComplementId(String value)
+ {
+ this.complementId = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures()
+ {
+ if (showComplementFeatures == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeatures;
+ }
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value)
+ {
+ this.showComplementFeatures = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop()
+ {
+ if (showComplementFeaturesOnTop == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeaturesOnTop;
+ }
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value)
+ {
+ this.showComplementFeaturesOnTop = value;
+ }
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Conservation shading increment
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getConsThreshold()
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value) {
- this.pidSelected = value;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Percent Identity Threshold
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getPidThreshold()
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Secondary structure consensus shading - since 2.11.4
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isSecstrSelected() {
- if (secstrSelected == null) {
- return false;
- } else {
- return secstrSelected;
- }
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = value;
+ }
- /**
- * Sets the value of the secstrSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isSecstrSelected()
- */
- public void setSecstrSelected(Boolean value) {
- this.secstrSelected = value;
- }
+ /**
+ * Conservation shading increment
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Secondary structure consensus increment
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSecstrThreshold() {
- return secstrThreshold;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getConsThreshold()
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- /**
- * Sets the value of the secstrThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- * @see #getSecstrThreshold()
- */
- public void setSecstrThreshold(Integer value) {
- this.secstrThreshold = value;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value)
+ {
+ this.pidSelected = value;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Percent Identity Threshold
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getPidThreshold()
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ /**
+ * Secondary structure consensus shading - since 2.11.4
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isSecstrSelected()
+ {
+ if (secstrSelected == null)
+ {
+ return false;
+ }
+ else
+ {
+ return secstrSelected;
+ }
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the secstrSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isSecstrSelected()
+ */
+ public void setSecstrSelected(Boolean value)
+ {
+ this.secstrSelected = value;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Secondary structure consensus increment
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSecstrThreshold()
+ {
+ return secstrThreshold;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Sets the value of the secstrThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ * @see #getSecstrThreshold()
+ */
+ public void setSecstrThreshold(Integer value)
+ {
+ this.secstrThreshold = value;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam
- extends WebServiceParameterSet
- {
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * handle for the calculation which uses
- * this parameter set
- *
- */
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
- /**
- * should the calculation be performed
- * immediately after loading in order to refresh results
- *
- */
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
- /**
- * should the calculation be automatically
- * performed on edits
- *
- */
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * handle for the calculation which uses
- * this parameter set
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCalcId() {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getCalcId()
- */
- public void setCalcId(String value) {
- this.calcId = value;
- }
-
- /**
- * should the calculation be performed
- * immediately after loading in order to refresh results
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNeedsUpdate() {
- if (needsUpdate == null) {
- return false;
- } else {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isNeedsUpdate()
- */
- public void setNeedsUpdate(Boolean value) {
- this.needsUpdate = value;
- }
-
- /**
- * should the calculation be automatically
- * performed on edits
- *
- */
- public boolean isAutoUpdate() {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value) {
- this.autoUpdate = value;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns {
-
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ /**
+ * handle for the calculation which uses this parameter set
+ *
+ */
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+
+ /**
+ * should the calculation be performed immediately after loading in order
+ * to refresh results
+ *
+ */
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+
+ /**
+ * should the calculation be automatically performed on edits
+ *
+ */
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * handle for the calculation which uses this parameter set
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getCalcId()
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * should the calculation be performed immediately after loading in order
+ * to refresh results
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate()
+ {
+ if (needsUpdate == null)
+ {
+ return false;
}
+ else
+ {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isNeedsUpdate()
+ */
+ public void setNeedsUpdate(Boolean value)
+ {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * should the calculation be automatically performed on edits
+ *
+ */
+ public boolean isAutoUpdate()
+ {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value)
+ {
+ this.autoUpdate = value;
+ }
+ }
- /**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Overview {
-
- @XmlAttribute(name = "showHidden")
- protected Boolean showHidden;
- @XmlAttribute(name = "residueColour")
- protected Integer residueColour;
- @XmlAttribute(name = "gapColour")
- protected Integer gapColour;
- @XmlAttribute(name = "hiddenColour")
- protected Integer hiddenColour;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the showHidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowHidden() {
- return showHidden;
- }
-
- /**
- * Sets the value of the showHidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowHidden(Boolean value) {
- this.showHidden = value;
- }
-
- /**
- * Gets the value of the residueColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getResidueColour() {
- return residueColour;
- }
-
- /**
- * Sets the value of the residueColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setResidueColour(Integer value) {
- this.residueColour = value;
- }
-
- /**
- * Gets the value of the gapColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGapColour() {
- return gapColour;
- }
-
- /**
- * Sets the value of the gapColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGapColour(Integer value) {
- this.gapColour = value;
- }
-
- /**
- * Gets the value of the hiddenColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHiddenColour() {
- return hiddenColour;
- }
-
- /**
- * Sets the value of the hiddenColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHiddenColour(Integer value) {
- this.hiddenColour = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview
+ {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden()
+ {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value)
+ {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getResidueColour()
+ {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value)
+ {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value)
+ {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value)
+ {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for JalviewUserColours complex type</p>.
+ * <p>
+ * Java class for JalviewUserColours complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="JalviewUserColours">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
- "version",
- "colour",
- "filter"
-})
-public class JalviewUserColours {
+@XmlType(
+ name = "JalviewUserColours",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "version", "colour", "filter" })
+public class JalviewUserColours
+{
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Colour> colour;
+
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Filter> filter;
+
+ @XmlAttribute(name = "schemeName")
+ protected String schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getVersion()
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the colour property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getColour().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Colour }
+ * </p>
+ *
+ *
+ * @return The value of the colour property.
+ */
+ public List<JalviewUserColours.Colour> getColour()
+ {
+ if (colour == null)
+ {
+ colour = new ArrayList<JalviewUserColours.Colour>();
+ }
+ return this.colour;
+ }
+
+ /**
+ * Gets the value of the filter property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the filter property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getFilter().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Filter }
+ * </p>
+ *
+ *
+ * @return The value of the filter property.
+ */
+ public List<JalviewUserColours.Filter> getFilter()
+ {
+ if (filter == null)
+ {
+ filter = new ArrayList<JalviewUserColours.Filter>();
+ }
+ return this.filter;
+ }
+
+ /**
+ * Gets the value of the schemeName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSchemeName()
+ {
+ return schemeName;
+ }
+
+ /**
+ * Sets the value of the schemeName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSchemeName(String value)
+ {
+ this.schemeName = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName" })
+ public static class Colour
+ {
/**
- * Jalview colour scheme document version.
+ * name of feature attribute to colour by, or attribute and sub-attribute
*
*/
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Colour> colour;
@XmlElement(namespace = "")
- protected List<JalviewUserColours.Filter> filter;
- @XmlAttribute(name = "schemeName")
- protected String schemeName;
+ protected List<String> attributeName;
/**
- * Jalview colour scheme document version.
+ * Single letter residue code for an alignment colour scheme, or feature
+ * type for a feature colour scheme
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
- }
+ @XmlAttribute(name = "Name")
+ protected String name;
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getVersion()
- */
- public void setVersion(String value) {
- this.version = value;
- }
+ @XmlAttribute(name = "RGB", required = true)
+ protected String rgb;
+
+ @XmlAttribute(name = "minRGB")
+ protected String minRGB;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshType")
+ protected ThresholdType threshType;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
/**
- * Gets the value of the colour property.
+ * name of feature attribute to colour by, or attribute and sub-attribute
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the colour property.</p>
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ * </p>
*
* <p>
* For example, to add a new item, do as follows:
* </p>
+ *
* <pre>
- * getColour().add(newItem);
+ * getAttributeName().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
+ * Objects of the following type(s) are allowed in the list {@link String }
* </p>
*
*
- * @return
- * The value of the colour property.
+ * @return The value of the attributeName property.
*/
- public List<JalviewUserColours.Colour> getColour() {
- if (colour == null) {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
}
/**
- * Gets the value of the filter property.
+ * Single letter residue code for an alignment colour scheme, or feature
+ * type for a feature colour scheme
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the filter property.</p>
+ * @return possible object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getFilter().add(newItem);
- * </pre>
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
*
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
- * </p>
+ * @see #getName()
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the rgb property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getRGB()
+ {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
*
+ * @param value
+ * allowed object is {@link String }
*
- * @return
- * The value of the filter property.
*/
- public List<JalviewUserColours.Filter> getFilter() {
- if (filter == null) {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
+ public void setRGB(String value)
+ {
+ this.rgb = value;
}
/**
- * Gets the value of the schemeName property.
+ * Gets the value of the minRGB property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getSchemeName() {
- return schemeName;
+ public String getMinRGB()
+ {
+ return minRGB;
}
/**
- * Sets the value of the schemeName property.
+ * Sets the value of the minRGB property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setSchemeName(String value) {
- this.schemeName = value;
+ public void setMinRGB(String value)
+ {
+ this.minRGB = value;
}
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * Sets the value of the noValueColour property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @param value
+ * allowed object is {@link NoValueColour }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * </sequence>
- * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshType property.
*
+ * @return possible object is {@link ThresholdType }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName"
- })
- public static class Colour {
-
- /**
- * name of feature attribute to colour by, or attribute and sub-attribute
- *
- */
- @XmlElement(namespace = "")
- protected List<String> attributeName;
- /**
- * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
- *
- */
- @XmlAttribute(name = "Name")
- protected String name;
- @XmlAttribute(name = "RGB", required = true)
- protected String rgb;
- @XmlAttribute(name = "minRGB")
- protected String minRGB;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- @XmlAttribute(name = "threshType")
- protected ThresholdType threshType;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * name of feature attribute to colour by, or attribute and sub-attribute
- *
- * Gets the value of the attributeName property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the attributeName property.
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getName()
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the rgb property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRGB() {
- return rgb;
- }
-
- /**
- * Sets the value of the rgb property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRGB(String value) {
- this.rgb = value;
- }
-
- /**
- * Gets the value of the minRGB property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMinRGB() {
- return minRGB;
- }
-
- /**
- * Sets the value of the minRGB property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMinRGB(String value) {
- this.minRGB = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshType property.
- *
- * @return
- * possible object is
- * {@link ThresholdType }
- *
- */
- public ThresholdType getThreshType() {
- return threshType;
- }
-
- /**
- * Sets the value of the threshType property.
- *
- * @param value
- * allowed object is
- * {@link ThresholdType }
- *
- */
- public void setThreshType(ThresholdType value) {
- this.threshType = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ public ThresholdType getThreshType()
+ {
+ return threshType;
+ }
+ /**
+ * Sets the value of the threshType property.
+ *
+ * @param value
+ * allowed object is {@link ThresholdType }
+ *
+ */
+ public void setThreshType(ThresholdType value)
+ {
+ this.threshType = value;
}
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * Sets the value of the threshold property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @param value
+ * allowed object is {@link Float }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- * </sequence>
- * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
*
+ * @param value
+ * allowed object is {@link Float }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "matcherSet"
- })
- public static class Filter {
-
- @XmlElement(namespace = "", required = true)
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "featureType", required = true)
- protected String featureType;
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the featureType property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFeatureType() {
- return featureType;
- }
-
- /**
- * Sets the value of the featureType property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFeatureType(String value) {
- this.featureType = value;
- }
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
}
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ * </sequence>
+ * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "matcherSet" })
+ public static class Filter
+ {
+
+ @XmlElement(namespace = "", required = true)
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "featureType", required = true)
+ protected String featureType;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the featureType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFeatureType()
+ {
+ return featureType;
+ }
+
+ /**
+ * Sets the value of the featureType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFeatureType(String value)
+ {
+ this.featureType = value;
+ }
+
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
- * This effectively represents a java.util.MapList
- * object
+ * This effectively represents a java.util.MapList object
*
- * <p>Java class for mapListType complex type</p>.
+ * <p>
+ * Java class for mapListType complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="mapListType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
- "mapListFrom",
- "mapListTo"
-})
-@XmlSeeAlso({
- Mapping.class
-})
-public class MapListType {
+@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
+@XmlSeeAlso({ Mapping.class })
+public class MapListType
+{
- /**
- * a region from start to end inclusive
- *
- */
- protected List<MapListType.MapListFrom> mapListFrom;
- /**
- * a region from start to end inclusive
- *
- */
- protected List<MapListType.MapListTo> mapListTo;
- /**
- * number of dictionary symbol widths involved in
- * each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence).
- * This is optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- */
- @XmlAttribute(name = "mapFromUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapFromUnit;
- /**
- * number of dictionary symbol widths involved in
- * each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence).
- * This is optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
- *
- */
- @XmlAttribute(name = "mapToUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapToUnit;
+ /**
+ * a region from start to end inclusive
+ *
+ */
+ protected List<MapListType.MapListFrom> mapListFrom;
+
+ /**
+ * a region from start to end inclusive
+ *
+ */
+ protected List<MapListType.MapListTo> mapListTo;
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ *
+ */
+ @XmlAttribute(name = "mapFromUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapFromUnit;
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ *
+ */
+ @XmlAttribute(name = "mapToUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapToUnit;
+
+ /**
+ * a region from start to end inclusive
+ *
+ * Gets the value of the mapListFrom property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the mapListFrom property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getMapListFrom().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListFrom }
+ * </p>
+ *
+ *
+ * @return The value of the mapListFrom property.
+ */
+ public List<MapListType.MapListFrom> getMapListFrom()
+ {
+ if (mapListFrom == null)
+ {
+ mapListFrom = new ArrayList<MapListType.MapListFrom>();
+ }
+ return this.mapListFrom;
+ }
+
+ /**
+ * a region from start to end inclusive
+ *
+ * Gets the value of the mapListTo property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the mapListTo property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getMapListTo().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListTo }
+ * </p>
+ *
+ *
+ * @return The value of the mapListTo property.
+ */
+ public List<MapListType.MapListTo> getMapListTo()
+ {
+ if (mapListTo == null)
+ {
+ mapListTo = new ArrayList<MapListType.MapListTo>();
+ }
+ return this.mapListTo;
+ }
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getMapFromUnit()
+ {
+ return mapFromUnit;
+ }
+
+ /**
+ * Sets the value of the mapFromUnit property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ * @see #getMapFromUnit()
+ */
+ public void setMapFromUnit(BigInteger value)
+ {
+ this.mapFromUnit = value;
+ }
+
+ /**
+ * number of dictionary symbol widths involved in each mapped position on this
+ * sequence (for example, 3 for a dna sequence exon region that is being
+ * mapped to a protein sequence). This is optional, since the unit can be
+ * usually be inferred from the dictionary type of each sequence involved in
+ * the mapping.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getMapToUnit()
+ {
+ return mapToUnit;
+ }
+
+ /**
+ * Sets the value of the mapToUnit property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ * @see #getMapToUnit()
+ */
+ public void setMapToUnit(BigInteger value)
+ {
+ this.mapToUnit = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListFrom
+ {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
/**
- * a region from start to end inclusive
- *
- * Gets the value of the mapListFrom property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getMapListFrom().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListFrom }
- * </p>
+ * Gets the value of the start property.
*
- *
- * @return
- * The value of the mapListFrom property.
*/
- public List<MapListType.MapListFrom> getMapListFrom() {
- if (mapListFrom == null) {
- mapListFrom = new ArrayList<MapListType.MapListFrom>();
- }
- return this.mapListFrom;
+ public int getStart()
+ {
+ return start;
}
/**
- * a region from start to end inclusive
- *
- * Gets the value of the mapListTo property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListTo property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getMapListTo().add(newItem);
- * </pre>
+ * Sets the value of the start property.
*
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListTo }
- * </p>
- *
- *
- * @return
- * The value of the mapListTo property.
*/
- public List<MapListType.MapListTo> getMapListTo() {
- if (mapListTo == null) {
- mapListTo = new ArrayList<MapListType.MapListTo>();
- }
- return this.mapListTo;
+ public void setStart(int value)
+ {
+ this.start = value;
}
/**
- * number of dictionary symbol widths involved in
- * each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence).
- * This is optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
+ * Gets the value of the end property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapFromUnit() {
- return mapFromUnit;
+ public int getEnd()
+ {
+ return end;
}
/**
- * Sets the value of the mapFromUnit property.
+ * Sets the value of the end property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- * @see #getMapFromUnit()
*/
- public void setMapFromUnit(BigInteger value) {
- this.mapFromUnit = value;
+ public void setEnd(int value)
+ {
+ this.end = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListTo
+ {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
/**
- * number of dictionary symbol widths involved in
- * each
- * mapped position on this sequence (for example, 3 for a dna
- * sequence exon
- * region that is being mapped to a protein sequence).
- * This is optional,
- * since the unit can be usually be inferred from the
- * dictionary type of
- * each sequence involved in the mapping.
+ * Gets the value of the start property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapToUnit() {
- return mapToUnit;
+ public int getStart()
+ {
+ return start;
}
/**
- * Sets the value of the mapToUnit property.
+ * Sets the value of the start property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- * @see #getMapToUnit()
*/
- public void setMapToUnit(BigInteger value) {
- this.mapToUnit = value;
+ public void setStart(int value)
+ {
+ this.start = value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * Gets the value of the end property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListFrom {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
+ public int getEnd()
+ {
+ return end;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * Sets the value of the end property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListTo {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
+ public void setEnd(int value)
+ {
+ this.end = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Defines a mapping from the local frame to a matrix
- * and its associated data specified by MatrixType
+ * Defines a mapping from the local frame to a matrix and its associated data
+ * specified by MatrixType
*
- * <p>Java class for MapOnAMatrixType complex type</p>.
+ * <p>
+ * Java class for MapOnAMatrixType complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="MapOnAMatrixType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MapOnAMatrixType", propOrder = {
- "property",
- "mapping"
-})
-public class MapOnAMatrixType {
+@XmlType(name = "MapOnAMatrixType", propOrder = { "property", "mapping" })
+public class MapOnAMatrixType
+{
- protected List<Property> property;
- /**
- * mapping from the matrix row and column positions
- * to
- * associated reference frame
- *
- */
- protected MapListType mapping;
- /**
- * reference to the matrix type this Map refers to
- *
- */
- @XmlAttribute(name = "matrix", required = true)
- protected String matrix;
- @XmlAttribute(name = "id")
- protected String id;
+ protected List<Property> property;
- /**
- * Gets the value of the property property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Property }
- * </p>
- *
- *
- * @return
- * The value of the property property.
- */
- public List<Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Property>();
- }
- return this.property;
- }
+ /**
+ * mapping from the matrix row and column positions to associated reference
+ * frame
+ *
+ */
+ protected MapListType mapping;
- /**
- * mapping from the matrix row and column positions
- * to
- * associated reference frame
- *
- * @return
- * possible object is
- * {@link MapListType }
- *
- */
- public MapListType getMapping() {
- return mapping;
- }
+ /**
+ * reference to the matrix type this Map refers to
+ *
+ */
+ @XmlAttribute(name = "matrix", required = true)
+ protected String matrix;
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link MapListType }
- *
- * @see #getMapping()
- */
- public void setMapping(MapListType value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * reference to the matrix type this Map refers to
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMatrix() {
- return matrix;
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Property }
+ * </p>
+ *
+ *
+ * @return The value of the property property.
+ */
+ public List<Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Property>();
}
+ return this.property;
+ }
- /**
- * Sets the value of the matrix property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getMatrix()
- */
- public void setMatrix(String value) {
- this.matrix = value;
- }
+ /**
+ * mapping from the matrix row and column positions to associated reference
+ * frame
+ *
+ * @return possible object is {@link MapListType }
+ *
+ */
+ public MapListType getMapping()
+ {
+ return mapping;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link MapListType }
+ *
+ * @see #getMapping()
+ */
+ public void setMapping(MapListType value)
+ {
+ this.mapping = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * reference to the matrix type this Map refers to
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMatrix()
+ {
+ return matrix;
+ }
+
+ /**
+ * Sets the value of the matrix property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getMatrix()
+ */
+ public void setMatrix(String value)
+ {
+ this.matrix = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Represent the jalview.datamodel.Mapping object -
- * it also provides
- * a way of storing sequences that are mapped 'to'
- * without adding them
- * to the sequence set (which will mean they are
- * then added to the alignment too).
+ * Represent the jalview.datamodel.Mapping object - it also provides a way of
+ * storing sequences that are mapped 'to' without adding them to the sequence
+ * set (which will mean they are then added to the alignment too).
*
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "dseqFor"
-})
+@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
@XmlRootElement(name = "Mapping")
-public class Mapping
- extends MapListType
+public class Mapping extends MapListType
{
- @XmlElement(name = "Sequence")
- protected Sequence sequence;
- protected String dseqFor;
- /**
- * Biotype of the mapping e.g. CdsToPeptide
- *
- */
- @XmlAttribute(name = "mappingType")
- protected String mappingType;
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+
+ protected String dseqFor;
+
+ /**
+ * Biotype of the mapping e.g. CdsToPeptide
+ *
+ */
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link Sequence }
- *
- */
- public Sequence getSequence() {
- return sequence;
- }
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link Sequence }
+ *
+ */
+ public Sequence getSequence()
+ {
+ return sequence;
+ }
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link Sequence }
- *
- */
- public void setSequence(Sequence value) {
- this.sequence = value;
- }
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value)
+ {
+ this.sequence = value;
+ }
- /**
- * Gets the value of the dseqFor property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDseqFor() {
- return dseqFor;
- }
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDseqFor()
+ {
+ return dseqFor;
+ }
- /**
- * Sets the value of the dseqFor property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDseqFor(String value) {
- this.dseqFor = value;
- }
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDseqFor(String value)
+ {
+ this.dseqFor = value;
+ }
- /**
- * Biotype of the mapping e.g. CdsToPeptide
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMappingType() {
- return mappingType;
- }
+ /**
+ * Biotype of the mapping e.g. CdsToPeptide
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMappingType()
+ {
+ return mappingType;
+ }
- /**
- * Sets the value of the mappingType property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getMappingType()
- */
- public void setMappingType(String value) {
- this.mappingType = value;
- }
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getMappingType()
+ */
+ public void setMappingType(String value)
+ {
+ this.mappingType = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Represents matrix data imported to Jalview, and the
- * results of any derived calculations (independent of a particular
- * view
- * on the matrix).
+ * Represents matrix data imported to Jalview, and the results of any derived
+ * calculations (independent of a particular view on the matrix).
*
- * <p>Java class for MatrixType complex type</p>.
+ * <p>
+ * Java class for MatrixType complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="MatrixType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
- "elements",
- "groups",
- "newick",
- "property"
-})
-public class MatrixType {
+@XmlType(
+ name = "MatrixType",
+ propOrder =
+ { "elements", "groups", "newick", "property" })
+public class MatrixType
+{
- /**
- * serialised representation of matrix as one or
- * more sets of comma separated values
- *
- */
- @XmlElement(required = true)
- protected String elements;
- /**
- * Comma separated series of longs formed from
- * bitsets defining partitions on the rows/columns of the matrix
- *
- */
- protected List<String> groups;
- /**
- * tree computed for this
- *
- */
- protected List<String> newick;
- protected List<Property> property;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "rows", required = true)
- protected BigInteger rows;
- @XmlAttribute(name = "cols", required = true)
- protected BigInteger cols;
- @XmlAttribute(name = "treeMethod")
- protected String treeMethod;
- @XmlAttribute(name = "cutHeight")
- protected Double cutHeight;
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ /**
+ * serialised representation of matrix as one or more sets of comma separated
+ * values
+ *
+ */
+ @XmlElement(required = true)
+ protected String elements;
- /**
- * serialised representation of matrix as one or
- * more sets of comma separated values
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getElements() {
- return elements;
- }
+ /**
+ * Comma separated series of longs formed from bitsets defining partitions on
+ * the rows/columns of the matrix
+ *
+ */
+ protected List<String> groups;
- /**
- * Sets the value of the elements property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getElements()
- */
- public void setElements(String value) {
- this.elements = value;
- }
+ /**
+ * tree computed for this
+ *
+ */
+ protected List<String> newick;
- /**
- * Comma separated series of longs formed from
- * bitsets defining partitions on the rows/columns of the matrix
- *
- * Gets the value of the groups property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the groups property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getGroups().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the groups property.
- */
- public List<String> getGroups() {
- if (groups == null) {
- groups = new ArrayList<String>();
- }
- return this.groups;
- }
+ protected List<Property> property;
- /**
- * tree computed for this
- *
- * Gets the value of the newick property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the newick property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getNewick().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the newick property.
- */
- public List<String> getNewick() {
- if (newick == null) {
- newick = new ArrayList<String>();
- }
- return this.newick;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the property property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Property }
- * </p>
- *
- *
- * @return
- * The value of the property property.
- */
- public List<Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Property>();
- }
- return this.property;
- }
+ @XmlAttribute(name = "rows", required = true)
+ protected BigInteger rows;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "cols", required = true)
+ protected BigInteger cols;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "treeMethod")
+ protected String treeMethod;
- /**
- * Gets the value of the rows property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getRows() {
- return rows;
- }
+ @XmlAttribute(name = "cutHeight")
+ protected Double cutHeight;
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setRows(BigInteger value) {
- this.rows = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the cols property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getCols() {
- return cols;
- }
+ /**
+ * serialised representation of matrix as one or more sets of comma separated
+ * values
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getElements()
+ {
+ return elements;
+ }
- /**
- * Sets the value of the cols property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setCols(BigInteger value) {
- this.cols = value;
- }
+ /**
+ * Sets the value of the elements property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getElements()
+ */
+ public void setElements(String value)
+ {
+ this.elements = value;
+ }
- /**
- * Gets the value of the treeMethod property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTreeMethod() {
- return treeMethod;
+ /**
+ * Comma separated series of longs formed from bitsets defining partitions on
+ * the rows/columns of the matrix
+ *
+ * Gets the value of the groups property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the groups property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getGroups().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the groups property.
+ */
+ public List<String> getGroups()
+ {
+ if (groups == null)
+ {
+ groups = new ArrayList<String>();
}
+ return this.groups;
+ }
- /**
- * Sets the value of the treeMethod property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTreeMethod(String value) {
- this.treeMethod = value;
+ /**
+ * tree computed for this
+ *
+ * Gets the value of the newick property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the newick property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getNewick().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the newick property.
+ */
+ public List<String> getNewick()
+ {
+ if (newick == null)
+ {
+ newick = new ArrayList<String>();
}
+ return this.newick;
+ }
- /**
- * Gets the value of the cutHeight property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getCutHeight() {
- return cutHeight;
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Property }
+ * </p>
+ *
+ *
+ * @return The value of the property property.
+ */
+ public List<Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Property>();
}
+ return this.property;
+ }
- /**
- * Sets the value of the cutHeight property.
- *
- * @param value
- * allowed object is
- * {@link Double }
- *
- */
- public void setCutHeight(Double value) {
- this.cutHeight = value;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getRows()
+ {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setRows(BigInteger value)
+ {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the cols property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getCols()
+ {
+ return cols;
+ }
+
+ /**
+ * Sets the value of the cols property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setCols(BigInteger value)
+ {
+ this.cols = value;
+ }
+
+ /**
+ * Gets the value of the treeMethod property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTreeMethod()
+ {
+ return treeMethod;
+ }
+
+ /**
+ * Sets the value of the treeMethod property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTreeMethod(String value)
+ {
+ this.treeMethod = value;
+ }
+
+ /**
+ * Gets the value of the cutHeight property.
+ *
+ * @return possible object is {@link Double }
+ *
+ */
+ public Double getCutHeight()
+ {
+ return cutHeight;
+ }
+
+ /**
+ * Sets the value of the cutHeight property.
+ *
+ * @param value
+ * allowed object is {@link Double }
+ *
+ */
+ public void setCutHeight(Double value)
+ {
+ this.cutHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
-
/**
* Graduated feature colour if no score (or attribute) value
*
- * <p>Java class for NoValueColour</p>.
+ * <p>
+ * Java class for NoValueColour
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
* <pre>
* <simpleType name="NoValueColour">
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum NoValueColour {
+public enum NoValueColour
+{
- @XmlEnumValue("None")
- NONE("None"),
- @XmlEnumValue("Min")
- MIN("Min"),
- @XmlEnumValue("Max")
- MAX("Max");
- private final String value;
+ @XmlEnumValue("None")
+ NONE("None"), @XmlEnumValue("Min")
+ MIN("Min"), @XmlEnumValue("Max")
+ MAX("Max");
- NoValueColour(String v) {
- value = v;
- }
+ private final String value;
- /**
- * Gets the value associated to the enum constant.
- *
- * @return
- * The value linked to the enum.
- */
- public String value() {
- return value;
- }
+ NoValueColour(String v)
+ {
+ value = v;
+ }
+
+ /**
+ * Gets the value associated to the enum constant.
+ *
+ * @return The value linked to the enum.
+ */
+ public String value()
+ {
+ return value;
+ }
- /**
- * Gets the enum associated to the value passed as parameter.
- *
- * @param v
- * The value to get the enum from.
- * @return
- * The enum which corresponds to the value, if it exists.
- * @throws IllegalArgumentException
- * If no value matches in the enum declaration.
- */
- public static NoValueColour fromValue(String v) {
- for (NoValueColour c: NoValueColour.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+ /**
+ * Gets the enum associated to the value passed as parameter.
+ *
+ * @param v
+ * The value to get the enum from.
+ * @return The enum which corresponds to the value, if it exists.
+ * @throws IllegalArgumentException
+ * If no value matches in the enum declaration.
+ */
+ public static NoValueColour fromValue(String v)
+ {
+ for (NoValueColour c : NoValueColour.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.jalview package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory {
-
- private static final QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
- private static final QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
- private static final QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link MapListType }
- *
- */
- public MapListType createMapListType() {
- return new MapListType();
- }
-
- /**
- * Create an instance of {@link Sequence }
- *
- */
- public Sequence createSequence() {
- return new Sequence();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame() {
- return new AlcodonFrame();
- }
-
- /**
- * Create an instance of {@link Annotation }
- *
- */
- public Annotation createAnnotation() {
- return new Annotation();
- }
-
- /**
- * Create an instance of {@link SequenceSet }
- *
- */
- public SequenceSet createSequenceSet() {
- return new SequenceSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet createFeatureMatcherSet() {
- return new FeatureMatcherSet();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours }
- *
- */
- public JalviewUserColours createJalviewUserColours() {
- return new JalviewUserColours();
- }
-
- /**
- * Create an instance of {@link Pdbentry }
- *
- */
- public Pdbentry createPdbentry() {
- return new Pdbentry();
- }
-
- /**
- * Create an instance of {@link Feature }
- *
- */
- public Feature createFeature() {
- return new Feature();
- }
-
- /**
- * Create an instance of {@link JalviewModel }
- *
- */
- public JalviewModel createJalviewModel() {
- return new JalviewModel();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
- return new JalviewModel.FeatureSettings();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer }
- *
- */
- public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
- return new JalviewModel.PcaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport }
- *
- */
- public JalviewModel.Viewport createJalviewModelViewport() {
- return new JalviewModel.Viewport();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq }
- *
- */
- public JalviewModel.JSeq createJalviewModelJSeq() {
- return new JalviewModel.JSeq();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
- *
- */
- public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
- return new JalviewModel.JSeq.RnaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids }
- *
- */
- public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
- return new JalviewModel.JSeq.Pdbids();
- }
-
- /**
- * Create an instance of {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme createAnnotationColourScheme() {
- return new AnnotationColourScheme();
- }
-
- /**
- * Create an instance of {@link PcaDataType }
- *
- */
- public PcaDataType createPcaDataType() {
- return new PcaDataType();
- }
-
- /**
- * Create an instance of {@link DoubleVector }
- *
- */
- public DoubleVector createDoubleVector() {
- return new DoubleVector();
- }
-
- /**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix() {
- return new DoubleMatrix();
- }
-
- /**
- * Create an instance of {@link Mapping }
- *
- */
- public Mapping createMapping() {
- return new Mapping();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListFrom }
- *
- */
- public MapListType.MapListFrom createMapListTypeMapListFrom() {
- return new MapListType.MapListFrom();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListTo }
- *
- */
- public MapListType.MapListTo createMapListTypeMapListTo() {
- return new MapListType.MapListTo();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType() {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Sequence.DBRef }
- *
- */
- public Sequence.DBRef createSequenceDBRef() {
- return new Sequence.DBRef();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
- *
- */
- public AnnotationElement createAnnotationElement() {
- return new AnnotationElement();
- }
-
- /**
- * Create an instance of {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine createAnnotationThresholdLine() {
- return new Annotation.ThresholdLine();
- }
-
- /**
- * Create an instance of {@link MapOnAMatrixType }
- *
- */
- public MapOnAMatrixType createMapOnAMatrixType() {
- return new MapOnAMatrixType();
- }
-
- /**
- * Create an instance of {@link jalview.xml.binding.jalview.Property }
- *
- */
- public jalview.xml.binding.jalview.Property createProperty() {
- return new jalview.xml.binding.jalview.Property();
- }
-
- /**
- * Create an instance of {@link SequenceSet.SequenceSetProperties }
- *
- */
- public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
- return new SequenceSet.SequenceSetProperties();
- }
-
- /**
- * Create an instance of {@link MatrixType }
- *
- */
- public MatrixType createMatrixType() {
- return new MatrixType();
- }
-
- /**
- * Create an instance of {@link VAMSAS }
- *
- */
- public VAMSAS createVAMSAS() {
- return new VAMSAS();
- }
-
- /**
- * Create an instance of {@link FeatureMatcher }
- *
- */
- public FeatureMatcher createFeatureMatcher() {
- return new FeatureMatcher();
- }
-
- /**
- * Create an instance of {@link WebServiceParameterSet }
- *
- */
- public WebServiceParameterSet createWebServiceParameterSet() {
- return new WebServiceParameterSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
- return new FeatureMatcherSet.CompoundMatcher();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Colour }
- *
- */
- public JalviewUserColours.Colour createJalviewUserColoursColour() {
- return new JalviewUserColours.Colour();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Filter }
- *
- */
- public JalviewUserColours.Filter createJalviewUserColoursFilter() {
- return new JalviewUserColours.Filter();
- }
-
- /**
- * Create an instance of {@link Pdbentry.Property }
- *
- */
- public Pdbentry.Property createPdbentryProperty() {
- return new Pdbentry.Property();
- }
-
- /**
- * Create an instance of {@link Feature.OtherData }
- *
- */
- public Feature.OtherData createFeatureOtherData() {
- return new Feature.OtherData();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JGroup }
- *
- */
- public JalviewModel.JGroup createJalviewModelJGroup() {
- return new JalviewModel.JGroup();
- }
-
- /**
- * Create an instance of {@link JalviewModel.UserColours }
- *
- */
- public JalviewModel.UserColours createJalviewModelUserColours() {
- return new JalviewModel.UserColours();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Tree }
- *
- */
- public JalviewModel.Tree createJalviewModelTree() {
- return new JalviewModel.Tree();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
- *
- */
- public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
- return new JalviewModel.FeatureSettings.Setting();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Group }
- *
- */
- public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
- return new JalviewModel.FeatureSettings.Group();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
- *
- */
- public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
- return new JalviewModel.PcaViewer.SequencePoint();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.Axis }
- *
- */
- public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
- return new JalviewModel.PcaViewer.Axis();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
- return new JalviewModel.PcaViewer.SeqPointMin();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
- return new JalviewModel.PcaViewer.SeqPointMax();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
- *
- */
- public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
- return new JalviewModel.Viewport.HiddenColumns();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
- *
- */
- public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
- return new JalviewModel.Viewport.CalcIdParam();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
- return new JalviewModel.Viewport.Overview();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- */
- public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
- return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- */
- public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
- return new JalviewModel.JSeq.Pdbids.StructureState();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
- public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
- return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
- public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
- return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
- return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
- }
+public class ObjectFactory
+{
+
+ private static final QName _JalviewModel_QNAME = new QName(
+ "www.jalview.org", "JalviewModel");
+
+ private static final QName _JalviewUserColours_QNAME = new QName(
+ "www.jalview.org/colours", "JalviewUserColours");
+
+ private static final QName _WebServiceParameterSet_QNAME = new QName(
+ "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType()
+ {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence()
+ {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame()
+ {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation()
+ {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet()
+ {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet()
+ {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours()
+ {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry()
+ {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature()
+ {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel()
+ {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
+ {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer()
+ {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport()
+ {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq()
+ {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
+ {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
+ {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme()
+ {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType()
+ {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector()
+ {
+ return new DoubleVector();
+ }
+
+ /**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix()
+ {
+ return new DoubleMatrix();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping()
+ {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom()
+ {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo()
+ {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType()
+ {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef()
+ {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+ {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+ {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement()
+ {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine()
+ {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link MapOnAMatrixType }
+ *
+ */
+ public MapOnAMatrixType createMapOnAMatrixType()
+ {
+ return new MapOnAMatrixType();
+ }
+
+ /**
+ * Create an instance of {@link jalview.xml.binding.jalview.Property }
+ *
+ */
+ public jalview.xml.binding.jalview.Property createProperty()
+ {
+ return new jalview.xml.binding.jalview.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
+ {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link MatrixType }
+ *
+ */
+ public MatrixType createMatrixType()
+ {
+ return new MatrixType();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS()
+ {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher()
+ {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet()
+ {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
+ {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour()
+ {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter()
+ {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty()
+ {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData()
+ {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup()
+ {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours()
+ {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree()
+ {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
+ {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
+ {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
+ {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
+ {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
+ {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
+ {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
+ {
+ return new JalviewModel.Viewport.Overview();
+ }
+
+ /**
+ * Create an instance of
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
+ {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
+ {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
+ * }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewModel }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
+ {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
+ JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/colours",
+ name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(
+ JalviewUserColours value)
+ {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
+ JalviewUserColours.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/xml/wsparamset",
+ name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
+ WebServiceParameterSet value)
+ {
+ return new JAXBElement<WebServiceParameterSet>(
+ _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+ null, value);
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* The results of a PCA calculation
*
- * <p>Java class for PcaDataType complex type</p>.
+ * <p>
+ * Java class for PcaDataType complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="PcaDataType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
- "pairwiseMatrix",
- "tridiagonalMatrix",
- "eigenMatrix"
-})
-public class PcaDataType {
+@XmlType(
+ name = "PcaDataType",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
+public class PcaDataType
+{
+
+ @XmlElement(required = true)
+ protected DoubleMatrix pairwiseMatrix;
+
+ @XmlElement(required = true)
+ protected DoubleMatrix tridiagonalMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix pairwiseMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix tridiagonalMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix eigenMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix eigenMatrix;
- /**
- * Gets the value of the pairwiseMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getPairwiseMatrix() {
- return pairwiseMatrix;
- }
+ /**
+ * Gets the value of the pairwiseMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getPairwiseMatrix()
+ {
+ return pairwiseMatrix;
+ }
- /**
- * Sets the value of the pairwiseMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setPairwiseMatrix(DoubleMatrix value) {
- this.pairwiseMatrix = value;
- }
+ /**
+ * Sets the value of the pairwiseMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setPairwiseMatrix(DoubleMatrix value)
+ {
+ this.pairwiseMatrix = value;
+ }
- /**
- * Gets the value of the tridiagonalMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getTridiagonalMatrix() {
- return tridiagonalMatrix;
- }
+ /**
+ * Gets the value of the tridiagonalMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getTridiagonalMatrix()
+ {
+ return tridiagonalMatrix;
+ }
- /**
- * Sets the value of the tridiagonalMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setTridiagonalMatrix(DoubleMatrix value) {
- this.tridiagonalMatrix = value;
- }
+ /**
+ * Sets the value of the tridiagonalMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setTridiagonalMatrix(DoubleMatrix value)
+ {
+ this.tridiagonalMatrix = value;
+ }
- /**
- * Gets the value of the eigenMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getEigenMatrix() {
- return eigenMatrix;
- }
+ /**
+ * Gets the value of the eigenMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getEigenMatrix()
+ {
+ return eigenMatrix;
+ }
- /**
- * Sets the value of the eigenMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setEigenMatrix(DoubleMatrix value) {
- this.eigenMatrix = value;
- }
+ /**
+ * Sets the value of the eigenMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setEigenMatrix(DoubleMatrix value)
+ {
+ this.eigenMatrix = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for pdbentry complex type</p>.
+ * <p>
+ * Java class for pdbentry complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="pdbentry">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
- "property"
-})
-@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
-})
-public class Pdbentry {
-
- protected List<Pdbentry.Property> property;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "file")
- protected String file;
+@XmlType(
+ name = "pdbentry",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "property" })
+@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
+public class Pdbentry
+{
- /**
- * Gets the value of the property property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Pdbentry.Property }
- * </p>
- *
- *
- * @return
- * The value of the property property.
- */
- public List<Pdbentry.Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Pdbentry.Property>();
- }
- return this.property;
- }
+ protected List<Pdbentry.Property> property;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "file")
+ protected String file;
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Pdbentry.Property }
+ * </p>
+ *
+ *
+ * @return The value of the property property.
+ */
+ public List<Pdbentry.Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Pdbentry.Property>();
}
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the file property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFile()
+ {
+ return file;
+ }
+
+ /**
+ * Sets the value of the file property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFile(String value)
+ {
+ this.file = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the type property.
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the file property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFile() {
- return file;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the file property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setFile(String value) {
- this.file = value;
+ public String getValue()
+ {
+ return value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "value", required = true)
- protected String value;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for property complex type</p>.
+ * <p>
+ * Java class for property complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="property">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "property")
-public class Property {
+public class Property
+{
+
+ @XmlAttribute(name = "name")
+ protected String name;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "value")
- protected String value;
+ @XmlAttribute(name = "value")
+ protected String value;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "dbRef"
-})
+@XmlType(name = "", propOrder = { "dbRef" })
@XmlRootElement(name = "Sequence")
-public class Sequence
- extends SequenceType
+public class Sequence extends SequenceType
{
- @XmlElement(name = "DBRef")
- protected List<Sequence.DBRef> dbRef;
+ @XmlElement(name = "DBRef")
+ protected List<Sequence.DBRef> dbRef;
+
+ /**
+ * dataset sequence id for this sequence. Will be created as union of
+ * sequences.
+ *
+ */
+ @XmlAttribute(name = "dsseqid")
+ protected String dsseqid;
+
+ /**
+ * Biotype of the sequence (if known)
+ *
+ */
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
+
+ /**
+ * Gets the value of the dbRef property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the dbRef property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getDBRef().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence.DBRef }
+ * </p>
+ *
+ *
+ * @return The value of the dbRef property.
+ */
+ public List<Sequence.DBRef> getDBRef()
+ {
+ if (dbRef == null)
+ {
+ dbRef = new ArrayList<Sequence.DBRef>();
+ }
+ return this.dbRef;
+ }
+
+ /**
+ * dataset sequence id for this sequence. Will be created as union of
+ * sequences.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDsseqid()
+ {
+ return dsseqid;
+ }
+
+ /**
+ * Sets the value of the dsseqid property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getDsseqid()
+ */
+ public void setDsseqid(String value)
+ {
+ this.dsseqid = value;
+ }
+
+ /**
+ * Biotype of the sequence (if known)
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBiotype()
+ {
+ return biotype;
+ }
+
+ /**
+ * Sets the value of the biotype property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getBiotype()
+ */
+ public void setBiotype(String value)
+ {
+ this.biotype = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "mapping" })
+ public static class DBRef
+ {
+
+ @XmlElement(name = "Mapping")
+ protected Mapping mapping;
+
+ @XmlAttribute(name = "source")
+ protected String source;
+
+ @XmlAttribute(name = "version")
+ protected String version;
+
+ @XmlAttribute(name = "accessionId")
+ protected String accessionId;
+
/**
- * dataset sequence id for this sequence. Will be
- * created as union of sequences.
+ * true for gene locus mapping, source=species, version=assembly,
+ * accession=chromosome
*
*/
- @XmlAttribute(name = "dsseqid")
- protected String dsseqid;
+ @XmlAttribute(name = "locus")
+ protected Boolean locus;
+
/**
- * Biotype of the sequence (if known)
+ * true for the representative accession for databases where multiple
+ * accessions map to the same entry (eg. Uniprot)
*
*/
- @XmlAttribute(name = "biotype")
- protected String biotype;
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
/**
- * Gets the value of the dbRef property.
+ * Gets the value of the mapping property.
*
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbRef property.</p>
+ * @return possible object is {@link Mapping }
*
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getDBRef().add(newItem);
- * </pre>
+ */
+ public Mapping getMapping()
+ {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value)
+ {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the source property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence.DBRef }
- * </p>
+ */
+ public String getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
*
+ * @param value
+ * allowed object is {@link String }
*
- * @return
- * The value of the dbRef property.
*/
- public List<Sequence.DBRef> getDBRef() {
- if (dbRef == null) {
- dbRef = new ArrayList<Sequence.DBRef>();
- }
- return this.dbRef;
+ public void setSource(String value)
+ {
+ this.source = value;
}
/**
- * dataset sequence id for this sequence. Will be
- * created as union of sequences.
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDsseqid() {
- return dsseqid;
+ public String getVersion()
+ {
+ return version;
}
/**
- * Sets the value of the dsseqid property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- * @see #getDsseqid()
+ * allowed object is {@link String }
+ *
*/
- public void setDsseqid(String value) {
- this.dsseqid = value;
+ public void setVersion(String value)
+ {
+ this.version = value;
}
/**
- * Biotype of the sequence (if known)
+ * Gets the value of the accessionId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getBiotype() {
- return biotype;
+ public String getAccessionId()
+ {
+ return accessionId;
}
/**
- * Sets the value of the biotype property.
+ * Sets the value of the accessionId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- * @see #getBiotype()
+ * allowed object is {@link String }
+ *
*/
- public void setBiotype(String value) {
- this.biotype = value;
+ public void setAccessionId(String value)
+ {
+ this.accessionId = value;
}
+ /**
+ * true for gene locus mapping, source=species, version=assembly,
+ * accession=chromosome
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLocus()
+ {
+ if (locus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return locus;
+ }
+ }
/**
- * <p>Java class for anonymous complex type</p>.
+ * Sets the value of the locus property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- * </sequence>
- * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * @see #isLocus()
+ */
+ public void setLocus(Boolean value)
+ {
+ this.locus = value;
+ }
+
+ /**
+ * true for the representative accession for databases where multiple
+ * accessions map to the same entry (eg. Uniprot)
*
+ * @return possible object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapping"
- })
- public static class DBRef {
-
- @XmlElement(name = "Mapping")
- protected Mapping mapping;
- @XmlAttribute(name = "source")
- protected String source;
- @XmlAttribute(name = "version")
- protected String version;
- @XmlAttribute(name = "accessionId")
- protected String accessionId;
- /**
- * true for gene locus mapping, source=species,
- * version=assembly, accession=chromosome
- *
- */
- @XmlAttribute(name = "locus")
- protected Boolean locus;
- /**
- * true for the representative accession for
- * databases where multiple accessions map to the same entry
- * (eg. Uniprot)
- *
- */
- @XmlAttribute(name = "canonical")
- protected Boolean canonical;
-
- /**
- * Gets the value of the mapping property.
- *
- * @return
- * possible object is
- * {@link Mapping }
- *
- */
- public Mapping getMapping() {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link Mapping }
- *
- */
- public void setMapping(Mapping value) {
- this.mapping = value;
- }
-
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSource() {
- return source;
- }
-
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSource(String value) {
- this.source = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the accessionId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccessionId() {
- return accessionId;
- }
-
- /**
- * Sets the value of the accessionId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccessionId(String value) {
- this.accessionId = value;
- }
-
- /**
- * true for gene locus mapping, source=species,
- * version=assembly, accession=chromosome
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isLocus() {
- if (locus == null) {
- return false;
- } else {
- return locus;
- }
- }
-
- /**
- * Sets the value of the locus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isLocus()
- */
- public void setLocus(Boolean value) {
- this.locus = value;
- }
-
- /**
- * true for the representative accession for
- * databases where multiple accessions map to the same entry
- * (eg. Uniprot)
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCanonical() {
- if (canonical == null) {
- return false;
- } else {
- return canonical;
- }
- }
-
- /**
- * Sets the value of the canonical property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- * @see #isCanonical()
- */
- public void setCanonical(Boolean value) {
- this.canonical = value;
- }
+ public boolean isCanonical()
+ {
+ if (canonical == null)
+ {
+ return false;
+ }
+ else
+ {
+ return canonical;
+ }
+ }
+ /**
+ * Sets the value of the canonical property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ * @see #isCanonical()
+ */
+ public void setCanonical(Boolean value)
+ {
+ this.canonical = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type</p>.
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "annotation",
- "sequenceSetProperties",
- "alcodonFrame",
- "matrix"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame",
+ "matrix" })
@XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
- @XmlElement(name = "Sequence")
- protected List<Sequence> sequence;
- @XmlElement(name = "Annotation")
- protected List<Annotation> annotation;
- protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
- @XmlElement(name = "AlcodonFrame")
- protected List<AlcodonFrame> alcodonFrame;
- /**
- * Matrices referred to by this set of sequences.
- *
- */
- @XmlElement(name = "Matrix")
- protected List<MatrixType> matrix;
- @XmlAttribute(name = "gapChar", required = true)
- protected String gapChar;
- /**
- * reference to set where jalview will gather the
- * dataset sequences for all sequences in the set.
- *
- */
- @XmlAttribute(name = "datasetId")
- protected String datasetId;
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> sequence;
- /**
- * Gets the value of the sequence property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequence property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSequence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence }
- * </p>
- *
- *
- * @return
- * The value of the sequence property.
- */
- public List<Sequence> getSequence() {
- if (sequence == null) {
- sequence = new ArrayList<Sequence>();
- }
- return this.sequence;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+
+ /**
+ * Matrices referred to by this set of sequences.
+ *
+ */
+ @XmlElement(name = "Matrix")
+ protected List<MatrixType> matrix;
+
+ @XmlAttribute(name = "gapChar", required = true)
+ protected String gapChar;
+
+ /**
+ * reference to set where jalview will gather the dataset sequences for all
+ * sequences in the set.
+ *
+ */
+ @XmlAttribute(name = "datasetId")
+ protected String datasetId;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the sequence property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSequence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Sequence }
+ * </p>
+ *
+ *
+ * @return The value of the sequence property.
+ */
+ public List<Sequence> getSequence()
+ {
+ if (sequence == null)
+ {
+ sequence = new ArrayList<Sequence>();
}
+ return this.sequence;
+ }
- /**
- * Gets the value of the annotation property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotation property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAnnotation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Annotation }
- * </p>
- *
- *
- * @return
- * The value of the annotation property.
- */
- public List<Annotation> getAnnotation() {
- if (annotation == null) {
- annotation = new ArrayList<Annotation>();
- }
- return this.annotation;
+ /**
+ * Gets the value of the annotation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the annotation property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAnnotation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Annotation
+ * }
+ * </p>
+ *
+ *
+ * @return The value of the annotation property.
+ */
+ public List<Annotation> getAnnotation()
+ {
+ if (annotation == null)
+ {
+ annotation = new ArrayList<Annotation>();
}
+ return this.annotation;
+ }
- /**
- * Gets the value of the sequenceSetProperties property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSequenceSetProperties().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SequenceSet.SequenceSetProperties }
- * </p>
- *
- *
- * @return
- * The value of the sequenceSetProperties property.
- */
- public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
- if (sequenceSetProperties == null) {
- sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
- }
- return this.sequenceSetProperties;
+ /**
+ * Gets the value of the sequenceSetProperties property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the sequenceSetProperties property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSequenceSetProperties().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet.SequenceSetProperties }
+ * </p>
+ *
+ *
+ * @return The value of the sequenceSetProperties property.
+ */
+ public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
+ {
+ if (sequenceSetProperties == null)
+ {
+ sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
}
+ return this.sequenceSetProperties;
+ }
- /**
- * Gets the value of the alcodonFrame property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getAlcodonFrame().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame }
- * </p>
- *
- *
- * @return
- * The value of the alcodonFrame property.
- */
- public List<AlcodonFrame> getAlcodonFrame() {
- if (alcodonFrame == null) {
- alcodonFrame = new ArrayList<AlcodonFrame>();
- }
- return this.alcodonFrame;
+ /**
+ * Gets the value of the alcodonFrame property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alcodonFrame property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getAlcodonFrame().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame }
+ * </p>
+ *
+ *
+ * @return The value of the alcodonFrame property.
+ */
+ public List<AlcodonFrame> getAlcodonFrame()
+ {
+ if (alcodonFrame == null)
+ {
+ alcodonFrame = new ArrayList<AlcodonFrame>();
}
+ return this.alcodonFrame;
+ }
- /**
- * Matrices referred to by this set of sequences.
- *
- * Gets the value of the matrix property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matrix property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getMatrix().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MatrixType }
- * </p>
- *
- *
- * @return
- * The value of the matrix property.
- */
- public List<MatrixType> getMatrix() {
- if (matrix == null) {
- matrix = new ArrayList<MatrixType>();
- }
- return this.matrix;
+ /**
+ * Matrices referred to by this set of sequences.
+ *
+ * Gets the value of the matrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the matrix property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getMatrix().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link MatrixType
+ * }
+ * </p>
+ *
+ *
+ * @return The value of the matrix property.
+ */
+ public List<MatrixType> getMatrix()
+ {
+ if (matrix == null)
+ {
+ matrix = new ArrayList<MatrixType>();
}
+ return this.matrix;
+ }
+
+ /**
+ * Gets the value of the gapChar property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getGapChar()
+ {
+ return gapChar;
+ }
+
+ /**
+ * Sets the value of the gapChar property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setGapChar(String value)
+ {
+ this.gapChar = value;
+ }
+
+ /**
+ * reference to set where jalview will gather the dataset sequences for all
+ * sequences in the set.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDatasetId()
+ {
+ return datasetId;
+ }
+
+ /**
+ * Sets the value of the datasetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getDatasetId()
+ */
+ public void setDatasetId(String value)
+ {
+ this.datasetId = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type
+ * </p>
+ * .
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ * </p>
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties
+ {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+
+ @XmlAttribute(name = "value")
+ protected String value;
/**
- * Gets the value of the gapChar property.
+ * Gets the value of the key property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getGapChar() {
- return gapChar;
+ public String getKey()
+ {
+ return key;
}
/**
- * Sets the value of the gapChar property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGapChar(String value) {
- this.gapChar = value;
- }
-
- /**
- * reference to set where jalview will gather the
- * dataset sequences for all sequences in the set.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDatasetId() {
- return datasetId;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the datasetId property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getDatasetId()
*/
- public void setDatasetId(String value) {
- this.datasetId = value;
+ public String getValue()
+ {
+ return value;
}
-
/**
- * <p>Java class for anonymous complex type</p>.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequenceSetProperties {
-
- @XmlAttribute(name = "key")
- protected String key;
- @XmlAttribute(name = "value")
- protected String value;
-
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for SequenceType complex type</p>.
+ * <p>
+ * Java class for SequenceType complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="SequenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = {
- "sequence",
- "name"
-})
-@XmlSeeAlso({
- Sequence.class
-})
-public class SequenceType {
-
- protected String sequence;
- protected String name;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "description")
- protected String description;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
+@XmlSeeAlso({ Sequence.class })
+public class SequenceType
+{
+
+ protected String sequence;
+
+ protected String name;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequence(String value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Whether filter has a threshold, and if so is it
- * above or below
+ * Whether filter has a threshold, and if so is it above or below
+ *
+ * <p>
+ * Java class for ThresholdType
+ * </p>
+ * .
*
- * <p>Java class for ThresholdType</p>.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
* <pre>
* <simpleType name="ThresholdType">
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum ThresholdType {
+public enum ThresholdType
+{
- NONE,
- ABOVE,
- BELOW;
+ NONE, ABOVE, BELOW;
- public String value() {
- return name();
- }
+ public String value()
+ {
+ return name();
+ }
- public static ThresholdType fromValue(String v) {
- return valueOf(v);
- }
+ public static ThresholdType fromValue(String v)
+ {
+ return valueOf(v);
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for VAMSAS complex type</p>.
+ * <p>
+ * Java class for VAMSAS complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="VAMSAS">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
- "tree",
- "sequenceSet"
-})
-public class VAMSAS {
+@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
+public class VAMSAS
+{
+
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
- @XmlElement(name = "Tree")
- protected List<String> tree;
- @XmlElement(name = "SequenceSet")
- protected List<SequenceSet> sequenceSet;
+ @XmlElement(name = "SequenceSet")
+ protected List<SequenceSet> sequenceSet;
- /**
- * Gets the value of the tree property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getTree().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the tree property.
- */
- public List<String> getTree() {
- if (tree == null) {
- tree = new ArrayList<String>();
- }
- return this.tree;
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the tree property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the tree property.
+ */
+ public List<String> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<String>();
}
+ return this.tree;
+ }
- /**
- * Gets the value of the sequenceSet property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getSequenceSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SequenceSet }
- * </p>
- *
- *
- * @return
- * The value of the sequenceSet property.
- */
- public List<SequenceSet> getSequenceSet() {
- if (sequenceSet == null) {
- sequenceSet = new ArrayList<SequenceSet>();
- }
- return this.sequenceSet;
+ /**
+ * Gets the value of the sequenceSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the sequenceSet property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getSequenceSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link SequenceSet
+ * }
+ * </p>
+ *
+ *
+ * @return The value of the sequenceSet property.
+ */
+ public List<SequenceSet> getSequenceSet()
+ {
+ if (sequenceSet == null)
+ {
+ sequenceSet = new ArrayList<SequenceSet>();
}
+ return this.sequenceSet;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for WebServiceParameterSet complex type</p>.
+ * <p>
+ * Java class for WebServiceParameterSet complex type
+ * </p>
+ * .
*
- * <p>The following schema fragment specifies the expected content contained within this class.</p>
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * </p>
*
* <pre>
* <complexType name="WebServiceParameterSet">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
- "version",
- "description",
- "serviceURL",
- "parameters"
-})
+@XmlType(
+ name = "WebServiceParameterSet",
+ namespace = "www.jalview.org/xml/wsparamset",
+ propOrder =
+ { "version", "description", "serviceURL", "parameters" })
@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
-})
-public class WebServiceParameterSet {
-
- /**
- * A Jalview Web Service Parameter Set container
- * version number.
- * Version 1 created for storing Jaba user presets.
- *
- */
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- /**
- * Short description - as utf8 encoded text. This is
- * usually displayed
- * in the body of an HTML capable tooltip, so HTML tags may be embedded
- * using standard UTF8 encoding.
- *
- */
- @XmlElement(namespace = "")
- protected String description;
- /**
- * URL for which the parameter set is valid. Jalview will use it to
- * match up parameter sets to service instances that can parse the
- * parameter set payload.
- *
- */
- @XmlElement(namespace = "", required = true)
- @XmlSchemaType(name = "anyURI")
- protected List<String> serviceURL;
- /**
- * UTF8 encoded string to be processed into a specific web services'
- * parameter set. Note - newlines may be important to the structure
- * of this file.
- *
- */
- @XmlElement(namespace = "", required = true)
- protected String parameters;
- /**
- * The short name for the parameter set. This will be shown amongst the
- * other presets for the web service.
- *
- */
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * A Jalview Web Service Parameter Set container
- * version number.
- * Version 1 created for storing Jaba user presets.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getVersion()
- */
- public void setVersion(String value) {
- this.version = value;
- }
-
- /**
- * Short description - as utf8 encoded text. This is
- * usually displayed
- * in the body of an HTML capable tooltip, so HTML tags may be embedded
- * using standard UTF8 encoding.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getDescription()
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * URL for which the parameter set is valid. Jalview will use it to
- * match up parameter sets to service instances that can parse the
- * parameter set payload.
- *
- * Gets the value of the serviceURL property.
- *
- * <p>This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the serviceURL property.</p>
- *
- * <p>
- * For example, to add a new item, do as follows:
- * </p>
- * <pre>
- * getServiceURL().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- * </p>
- *
- *
- * @return
- * The value of the serviceURL property.
- */
- public List<String> getServiceURL() {
- if (serviceURL == null) {
- serviceURL = new ArrayList<String>();
- }
- return this.serviceURL;
- }
-
- /**
- * UTF8 encoded string to be processed into a specific web services'
- * parameter set. Note - newlines may be important to the structure
- * of this file.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getParameters() {
- return parameters;
- }
-
- /**
- * Sets the value of the parameters property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getParameters()
- */
- public void setParameters(String value) {
- this.parameters = value;
- }
-
- /**
- * The short name for the parameter set. This will be shown amongst the
- * other presets for the web service.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- * @see #getName()
- */
- public void setName(String value) {
- this.name = value;
+ jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
+public class WebServiceParameterSet
+{
+
+ /**
+ * A Jalview Web Service Parameter Set container version number. Version 1
+ * created for storing Jaba user presets.
+ *
+ */
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+
+ /**
+ * Short description - as utf8 encoded text. This is usually displayed in the
+ * body of an HTML capable tooltip, so HTML tags may be embedded using
+ * standard UTF8 encoding.
+ *
+ */
+ @XmlElement(namespace = "")
+ protected String description;
+
+ /**
+ * URL for which the parameter set is valid. Jalview will use it to match up
+ * parameter sets to service instances that can parse the parameter set
+ * payload.
+ *
+ */
+ @XmlElement(namespace = "", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected List<String> serviceURL;
+
+ /**
+ * UTF8 encoded string to be processed into a specific web services' parameter
+ * set. Note - newlines may be important to the structure of this file.
+ *
+ */
+ @XmlElement(namespace = "", required = true)
+ protected String parameters;
+
+ /**
+ * The short name for the parameter set. This will be shown amongst the other
+ * presets for the web service.
+ *
+ */
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * A Jalview Web Service Parameter Set container version number. Version 1
+ * created for storing Jaba user presets.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getVersion()
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Short description - as utf8 encoded text. This is usually displayed in the
+ * body of an HTML capable tooltip, so HTML tags may be embedded using
+ * standard UTF8 encoding.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getDescription()
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * URL for which the parameter set is valid. Jalview will use it to match up
+ * parameter sets to service instances that can parse the parameter set
+ * payload.
+ *
+ * Gets the value of the serviceURL property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the serviceURL property.
+ * </p>
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * </p>
+ *
+ * <pre>
+ * getServiceURL().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ * </p>
+ *
+ *
+ * @return The value of the serviceURL property.
+ */
+ public List<String> getServiceURL()
+ {
+ if (serviceURL == null)
+ {
+ serviceURL = new ArrayList<String>();
}
+ return this.serviceURL;
+ }
+
+ /**
+ * UTF8 encoded string to be processed into a specific web services' parameter
+ * set. Note - newlines may be important to the structure of this file.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getParameters()
+ {
+ return parameters;
+ }
+
+ /**
+ * Sets the value of the parameters property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getParameters()
+ */
+ public void setParameters(String value)
+ {
+ this.parameters = value;
+ }
+
+ /**
+ * The short name for the parameter set. This will be shown amongst the other
+ * presets for the web service.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ * @see #getName()
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
}
// Generated on: 2024.07.25 at 04:43:38 PM BST
//
-@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+ namespace = "www.vamsas.ac.uk/jalview/version2",
+ elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.jalview;
String s = "aArRnNzZxX *.-?";
assertArrayEquals(expected, as.indexEncode(s));
}
- @Test(groups= {"Functional"})
+
+ @Test(groups = { "Functional" })
public void testGlobalAlignment()
{
- String seq1="CAGCTAGCG",seq2="CCATACGA";
- Sequence sq1=new Sequence("s1",seq1),sq2=new Sequence("s2",seq2);
+ String seq1 = "CAGCTAGCG", seq2 = "CCATACGA";
+ Sequence sq1 = new Sequence("s1", seq1), sq2 = new Sequence("s2", seq2);
// AlignSeq doesn't report the unaligned regions at either end of sequences
- //String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
+ // String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
// so we check we have the aligned segment correct only
- String alseq1="CAGCTAGCG",alseq2="CA--TA-CG";
- AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1,sq2,AlignSeq.DNA);
- assertEquals(as.getAStr1()+"\n"+as.getAStr2(),alseq1+"\n"+alseq2);
+ String alseq1 = "CAGCTAGCG", alseq2 = "CA--TA-CG";
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1, sq2, AlignSeq.DNA);
+ assertEquals(as.getAStr1() + "\n" + as.getAStr2(),
+ alseq1 + "\n" + alseq2);
}
}
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure",
- new Annotation[] {});
- AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred",
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
new Annotation[] {});
AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
new Annotation[] {});
-
- AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] {ann1, ann3, ann4};
- AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] {ann2, ann3, ann4};
-
- AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] {ann3, ann4};
-
+ AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
+
AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
-
- AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] {ann1, ann2, ann3, ann4};
+
+ AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
+ ann3, ann4 };
}
@Test(groups = { "Functional" })
&& al.getAlignmentAnnotation().length == 2);
}
-
- @Test(groups = "Functional", dataProvider = "SecondaryStructureAnnotations")
- public void testSecondaryStructurePresentAndSources(AlignmentAnnotation[] annotations, boolean expectedSSPresent, ArrayList<String> expectedSSSources) {
- Assert.assertEquals(expectedSSPresent, AlignmentUtils.isSecondaryStructurePresent(annotations));
- }
- @DataProvider(name = "SecondaryStructureAnnotations")
- public static Object[][] provideSecondaryStructureAnnotations() {
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{});
- AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{});
- AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
- AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
-
- List<String> ssSources1 = new ArrayList<>(Arrays.asList("3D Structures"));
- List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
- List<String> ssSources3 = new ArrayList<>(Arrays.asList("3D Structures", "JPred"));
- List<String> ssSources4 = new ArrayList<>();
-
- return new Object[][]{
- {new AlignmentAnnotation[]{ann1, ann3, ann4}, true, ssSources1},
- {new AlignmentAnnotation[]{ann2, ann3, ann4}, true, ssSources2},
- {new AlignmentAnnotation[]{ann3, ann4}, false, ssSources4},
- {new AlignmentAnnotation[]{}, false, ssSources4},
- {new AlignmentAnnotation[]{ann1, ann2, ann3, ann4}, true, ssSources3}
- };
- }
-
- @Test(dataProvider = "SecondaryStructureAnnotationColours")
- public void testSecondaryStructureAnnotationColour(char symbol, Color expectedColor) {
- Color actualColor = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
- Assert.assertEquals(actualColor, expectedColor);
- }
+ @Test(
+ groups = "Functional",
+ dataProvider = "SecondaryStructureAnnotations")
+ public void testSecondaryStructurePresentAndSources(
+ AlignmentAnnotation[] annotations, boolean expectedSSPresent,
+ ArrayList<String> expectedSSSources)
+ {
+ Assert.assertEquals(expectedSSPresent,
+ AlignmentUtils.isSecondaryStructurePresent(annotations));
+ }
- @DataProvider(name = "SecondaryStructureAnnotationColours")
- public static Object[][] provideSecondaryStructureAnnotationColours() {
- return new Object[][]{
- {'C', Color.gray},
- {'E', Color.green},
- {'H', Color.red},
- {'-', Color.gray}
- };
- }
-
- @Test(dataProvider = "SSAnnotationPresence")
- public void testIsSSAnnotationPresent(Map<SequenceI, List<AlignmentAnnotation>> annotations, boolean expectedPresence) {
- boolean actualPresence = AlignmentUtils.isSSAnnotationPresent(annotations);
- Assert.assertEquals(actualPresence, expectedPresence);
- }
+ @DataProvider(name = "SecondaryStructureAnnotations")
+ public static Object[][] provideSecondaryStructureAnnotations()
+ {
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
+ new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
- @DataProvider(name = "SSAnnotationPresence")
- public static Object[][] provideSSAnnotationPresence() {
- Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
- SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
- List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
- annotationsList1.add(new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{}));
- annotations1.put(seq1, annotationsList1); // Annotation present secondary structure for seq1
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
- SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
- List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
- annotationsList2.add(new AlignmentAnnotation("Other Annotation", "Other Annotation", new Annotation[]{}));
- annotations2.put(seq2, annotationsList2); // Annotation not related to any of secondary structure for seq2
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
- // Empty annotation map
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
- SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
- annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{}));
- annotations4.put(seq4, annotationsList4); // Annotation present from JPred for seq4
-
-
- return new Object[][]{
- {annotations1, true}, // Annotations present secondary structure present
- {annotations2, false}, // No annotations related to any of the secondary structure present
- {annotations3, false}, // Empty annotation map
- {annotations4, true}, // Annotations present from JPred secondary structure present
- };
- }
-
- @Test
- public void testGetSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations, String expectedSSSource) {
- List<String> actualSSSource = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
- Assert.assertEquals(actualSSSource, expectedSSSource);
- }
-
- @DataProvider(name = "SSSourceFromAnnotationDescription")
- public static Object[][] provideSSSourceFromAnnotationDescription() {
- Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
- SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
- List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
- annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output", new Annotation[]{}));
- annotations1.put(seq1, annotationsList1); // Annotation present from JPred for seq1
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
- SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
- List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
- annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for af-q43517-f1A", new Annotation[]{}));
- annotations2.put(seq2, annotationsList2); // Annotation present secondary structure from Alphafold for seq2
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
- // Empty annotation map
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
- SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
- annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for 4zhpA", new Annotation[]{}));
- annotations4.put(seq4, annotationsList4); // Annotation present secondary structure from pdb for seq4
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
- SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
- annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
- new Annotation[]{}));
- annotations5.put(seq5, annotationsList5); // Annotation present secondary structure from Swiss model for seq5
-
-
- //JPred Output - JPred
- //Secondary Structure for af-q43517-f1A - Alphafold
- //Secondary Structure for 4zhpA - Experimental
- //Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P - Swiss Model
-
- return new Object[][]{
- {annotations1, "JPred"},
- {annotations2, "Alphafold"},
- {annotations3, null},
- {annotations4, "PDB"},
- {annotations5, "Swiss Model"}
- };
- }
+ List<String> ssSources1 = new ArrayList<>(
+ Arrays.asList("3D Structures"));
+ List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
+ List<String> ssSources3 = new ArrayList<>(
+ Arrays.asList("3D Structures", "JPred"));
+ List<String> ssSources4 = new ArrayList<>();
+
+ return new Object[][] {
+ { new AlignmentAnnotation[]
+ { ann1, ann3, ann4 }, true, ssSources1 },
+ { new AlignmentAnnotation[]
+ { ann2, ann3, ann4 }, true, ssSources2 },
+ { new AlignmentAnnotation[]
+ { ann3, ann4 }, false, ssSources4 },
+ { new AlignmentAnnotation[] {}, false, ssSources4 },
+ { new AlignmentAnnotation[]
+ { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
+ }
+
+ @Test(dataProvider = "SecondaryStructureAnnotationColours")
+ public void testSecondaryStructureAnnotationColour(char symbol,
+ Color expectedColor)
+ {
+ Color actualColor = AlignmentUtils
+ .getSecondaryStructureAnnotationColour(symbol);
+ Assert.assertEquals(actualColor, expectedColor);
+ }
+
+ @DataProvider(name = "SecondaryStructureAnnotationColours")
+ public static Object[][] provideSecondaryStructureAnnotationColours()
+ {
+ return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
+ { 'H', Color.red },
+ { '-', Color.gray } };
+ }
+
+ @Test(dataProvider = "SSAnnotationPresence")
+ public void testIsSSAnnotationPresent(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations,
+ boolean expectedPresence)
+ {
+ boolean actualPresence = AlignmentUtils
+ .isSSAnnotationPresent(annotations);
+ Assert.assertEquals(actualPresence, expectedPresence);
+ }
+
+ @DataProvider(name = "SSAnnotationPresence")
+ public static Object[][] provideSSAnnotationPresence()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure", new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present secondary
+ // structure for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Other Annotation",
+ "Other Annotation", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation not related to any
+ // of secondary structure for seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
+ new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present from JPred
+ // for seq4
+
+ return new Object[][] { { annotations1, true }, // Annotations present
+ // secondary structure
+ // present
+ { annotations2, false }, // No annotations related to any of the
+ // secondary structure present
+ { annotations3, false }, // Empty annotation map
+ { annotations4, true }, // Annotations present from JPred secondary
+ // structure present
+ };
+ }
+
+ @Test
+ public void testGetSSSourceFromAnnotationDescription(
+ AlignmentAnnotation[] annotations, String expectedSSSource)
+ {
+ List<String> actualSSSource = AlignmentUtils
+ .extractSSSourceInAlignmentAnnotation(annotations);
+ Assert.assertEquals(actualSSSource, expectedSSSource);
+ }
+
+ @DataProvider(name = "SSSourceFromAnnotationDescription")
+ public static Object[][] provideSSSourceFromAnnotationDescription()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
+ new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present from JPred
+ // for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation present secondary
+ // structure from Alphafold for
+ // seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for 4zhpA", new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present secondary
+ // structure from pdb for seq4
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
+ SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
+ annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
+ new Annotation[] {}));
+ annotations5.put(seq5, annotationsList5); // Annotation present secondary
+ // structure from Swiss model for
+ // seq5
+
+ // JPred Output - JPred
+ // Secondary Structure for af-q43517-f1A - Alphafold
+ // Secondary Structure for 4zhpA - Experimental
+ // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
+ // Swiss Model
+
+ return new Object[][] { { annotations1, "JPred" },
+ { annotations2, "Alphafold" },
+ { annotations3, null },
+ { annotations4, "PDB" },
+ { annotations5, "Swiss Model" } };
+ }
}
assertFalse(sm instanceof PairwiseScoreModelI);
assertTrue(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "Sequence Feature Similarity");
-
+
sm = models.next();
assertFalse(sm instanceof SimilarityScoreModel);
assertFalse(sm instanceof PairwiseScoreModelI);
// This class tests methods in Class SecondaryStructureDistanceModel
public class SecondaryStructureDistanceModelTest
{
-
+
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 1 + 0 = 1/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 0 + 0 = 0/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
-
+
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
-
/**
* <pre>
* Set up
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
-
+
/*
* Set up secondary structure annotations
*/
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
Annotation[] anns2;
-
+
/* All secondary structure annotations are similar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss E H S E
*/
- if(similar == "All Similar") {
-
- anns1 = new Annotation[] { ssE, ssH, ssC, ssE};
- anns2 = new Annotation[] { ssE, ssH, ssC, ssE};
-
+ if (similar == "All Similar")
+ {
+
+ anns1 = new Annotation[] { ssE, ssH, ssC, ssE };
+ anns2 = new Annotation[] { ssE, ssH, ssC, ssE };
+
}
-
+
/* All secondary structure annotations are dissimilar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss H E E C
*/
- else if(similar == "Not Similar") {
-
- anns1 = new Annotation[] { ssE, ssE, ssC, ssE};
- anns2 = new Annotation[] { ssH, ssH, ssE, ssC};
-
+ else if (similar == "Not Similar")
+ {
+
+ anns1 = new Annotation[] { ssE, ssE, ssC, ssE };
+ anns2 = new Annotation[] { ssH, ssH, ssE, ssC };
+
}
-
+
/* All secondary structure annotations are dissimilar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss H E E C
*/
- else if(similar == "With Coil") {
-
- anns1 = new Annotation[] { ssE, ssE, null, ssE};
- anns2 = new Annotation[] { ssH, ssH, ssE, null};
-
+ else if (similar == "With Coil")
+ {
+
+ anns1 = new Annotation[] { ssE, ssE, null, ssE };
+ anns2 = new Annotation[] { ssH, ssH, ssE, null };
+
}
-
+
/* Set up
* column 1 2 3 4
* seq s1 F R K S
* seq s2 F S J L
* ss H E E C
*/
- else {
-
- anns1 = new Annotation[] { ssH, ssE, ssC, ssE};
- anns2 = new Annotation[] { ssH, ssE, ssE, ssC};
+ else
+ {
+
+ anns1 = new Annotation[] { ssH, ssE, ssC, ssE };
+ anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
}
-
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
- AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns2);
-
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns2);
+
s1.addAlignmentAnnotation(ann1);
- s2.addAlignmentAnnotation(ann2);
-
+ s2.addAlignmentAnnotation(ann2);
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
return af;
}
-
/**
* <pre>
*/
protected AlignFrame setupAlignmentViewWithGap()
{
-
+
SequenceI s1 = new Sequence("s1", "FR S");
SequenceI s2 = new Sequence("s2", "FSJL");
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
-
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
Annotation[] anns2;
-
- anns1 = new Annotation[] { ssH, ssE, ssC};
- anns2 = new Annotation[] { ssH, ssE, ssE, ssC};
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
- AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns2);
-
+
+ anns1 = new Annotation[] { ssH, ssE, ssC };
+ anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns2);
+
s1.addAlignmentAnnotation(ann1);
- s2.addAlignmentAnnotation(ann2);
-
+ s2.addAlignmentAnnotation(ann2);
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
-
+
return af;
}
-
- protected AlignFrame setupAlignmentViewWithoutSS(String type) {
-
+
+ protected AlignFrame setupAlignmentViewWithoutSS(String type)
+ {
+
SequenceI s1 = new Sequence("s1", "FR S");
SequenceI s2 = new Sequence("s2", "FSJL");
-
+
s1.addSequenceFeature(
new SequenceFeature("chain", null, 1, 3, 0f, null));
s1.addSequenceFeature(
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
- if(!type.equals("both")) {
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+
+ if (!type.equals("both"))
+ {
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
-
- anns1 = new Annotation[] { ssH, ssE, ssC};
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
-
- s1.addAlignmentAnnotation(ann1);
+
+ anns1 = new Annotation[] { ssH, ssE, ssC };
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+
+ s1.addAlignmentAnnotation(ann1);
}
-
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
return af;
}
-
-
+
@DataProvider(name = "testData")
- public Object[][] testData() {
- return new Object[][] {
- {"All Similar", 1d, 1d, 0d, 0d / 4},
- {"Partially Similar", 1d, 1d, 0d, 0d},
- {"Not Similar", 1d, 1d, 0d, 0d},
- {"With Coil", 1d, 1d, 0d, 0d},
- };
+ public Object[][] testData()
+ {
+ return new Object[][] { { "All Similar", 1d, 1d, 0d, 0d / 4 },
+ { "Partially Similar", 1d, 1d, 0d, 0d },
+ { "Not Similar", 1d, 1d, 0d, 0d },
+ { "With Coil", 1d, 1d, 0d, 0d }, };
}
@Test(dataProvider = "testData")
- public void testFindDistances(String scenario, double expectedValue00, double expectedValue11,
- double expectedValue01, double expectedValue10) {
- AlignFrame af = setupAlignmentView(scenario);
- AlignViewport viewport = af.getViewport();
- AlignmentView view = viewport.getAlignmentView(false);
-
- ScoreModelI sm = new SecondaryStructureDistanceModel();
- sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
- af.alignPanel);
-
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
- params.setSecondaryStructureSource("3D Structures");
- MatrixI distances = sm.findDistances(view, params);
-
- assertEquals(distances.getValue(0, 0), expectedValue00);
- assertEquals(distances.getValue(1, 1), expectedValue11);
- assertEquals(distances.getValue(0, 1), expectedValue01);
- assertEquals(distances.getValue(1, 0), expectedValue10);
+ public void testFindDistances(String scenario, double expectedValue00,
+ double expectedValue11, double expectedValue01,
+ double expectedValue10)
+ {
+ AlignFrame af = setupAlignmentView(scenario);
+ AlignViewport viewport = af.getViewport();
+ AlignmentView view = viewport.getAlignmentView(false);
+
+ ScoreModelI sm = new SecondaryStructureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ af.alignPanel);
+
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
+ params.setSecondaryStructureSource("3D Structures");
+ MatrixI distances = sm.findDistances(view, params);
+
+ assertEquals(distances.getValue(0, 0), expectedValue00);
+ assertEquals(distances.getValue(1, 1), expectedValue11);
+ assertEquals(distances.getValue(0, 1), expectedValue01);
+ assertEquals(distances.getValue(1, 0), expectedValue10);
}
-
}
assertEquals(10, sf.getBegin());
assertEquals(11, sf.getEnd());
}
+
private SequenceI mkDs(SequenceI as)
{
SequenceI ds = as.createDatasetSequence();
ds.setSequence(ds.getSequenceAsString().toUpperCase(Locale.ROOT));
return ds;
}
+
/**
* Test that mimics 'remove all gapped columns' action. This generates a
* series Delete Gap edits that each act on all sequences that share a gapped
* and check we are preserving data - if the calls below fail, something has broken the Jalview dataset derivation process
*/
assertEquals("ABCDEF", seq1.getDatasetSequence().getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- SequenceI seq2 = new Sequence("sq2",original2);
+ assertEquals(original1, seq1.getSequenceAsString());
+ SequenceI seq2 = new Sequence("sq2", original2);
SequenceI ds2 = mkDs(seq2);
SequenceI seq3 = new Sequence("sq3", original3);
SequenceI ds3 = mkDs(seq3);
- List<SequenceI> sqs = Arrays.asList( seq1, seq2, seq3 );
+ List<SequenceI> sqs = Arrays.asList(seq1, seq2, seq3);
Alignment al = new Alignment(sqs.toArray(new SequenceI[0]));
- EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1, 7, al);
+ EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1,
+ 7, al);
String exp = "-ABcD---EF";
// check without case conservation
- assertEquals(exp.toUpperCase(Locale.ROOT),seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
+ assertEquals(exp.toUpperCase(Locale.ROOT),
+ seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
// check case
- assertEquals(exp,seq1.getSequenceAsString());
+ assertEquals(exp, seq1.getSequenceAsString());
// and other seqs
- assertEquals("-GHiJ---",seq2.getSequenceAsString());
- assertEquals("-MNoP---Q",seq3.getSequenceAsString());
- lefj.undoCommand(new AlignmentI[] { al});
- assertEquals(original3,seq3.getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- assertEquals(original2,seq2.getSequenceAsString());
-
- EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs, 2, 7, al);
- assertEquals("----ABcDEF",seq1.getSequenceAsString());
- assertEquals("-G---HiJ",seq2.getSequenceAsString());
- assertEquals("-M---NoPQ",seq3.getSequenceAsString());
- righj.undoCommand(new AlignmentI[] { al});
- assertEquals(original3,seq3.getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- assertEquals(original2,seq2.getSequenceAsString());
-
+ assertEquals("-GHiJ---", seq2.getSequenceAsString());
+ assertEquals("-MNoP---Q", seq3.getSequenceAsString());
+ lefj.undoCommand(new AlignmentI[] { al });
+ assertEquals(original3, seq3.getSequenceAsString());
+ assertEquals(original1, seq1.getSequenceAsString());
+ assertEquals(original2, seq2.getSequenceAsString());
+
+ EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs,
+ 2, 7, al);
+ assertEquals("----ABcDEF", seq1.getSequenceAsString());
+ assertEquals("-G---HiJ", seq2.getSequenceAsString());
+ assertEquals("-M---NoPQ", seq3.getSequenceAsString());
+ righj.undoCommand(new AlignmentI[] { al });
+ assertEquals(original3, seq3.getSequenceAsString());
+ assertEquals(original1, seq1.getSequenceAsString());
+ assertEquals(original2, seq2.getSequenceAsString());
+
}
}
*/
package jalview.gui;
-
import java.awt.Color;
import java.io.File;
import java.util.Iterator;
+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
- + "DQWNVEVY\n"
- + ">1GAQ|B/1-98\n"
+ + "DQWNVEVY\n" + ">1GAQ|B/1-98\n"
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
- + "WVLTCHAYPTSDVVIETHKEEELTGA\n"
- + ">1GAQ|C/19-314\n"
+ + "WVLTCHAYPTSDVVIETHKEEELTGA\n" + ">1GAQ|C/19-314\n"
+ "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
- + "DQWNVEVY\n"
- ,
- DataSourceType.PASTE);
+ + "DQWNVEVY\n", DataSourceType.PASTE);
/*
* wait for Consensus thread to complete
@Test(groups = "Functional")
public void testAssociatePDBFile()
{
- String assoc_file="examples/1gaq.txt";
- for (SequenceI toassoc:af.getViewport().getAlignment().getSequences())
+ String assoc_file = "examples/1gaq.txt";
+ for (SequenceI toassoc : af.getViewport().getAlignment().getSequences())
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(assoc_file,
- DataSourceType.FILE, toassoc, false,
- Desktop.instance);
+ PDBEntry pe = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ assoc_file, DataSourceType.FILE, toassoc, false,
+ Desktop.instance);
Assert.assertNotNull(pe);
- Assert.assertNotEquals(toassoc.getDatasetSequence().getAnnotation().length,0);
+ Assert.assertNotEquals(
+ toassoc.getDatasetSequence().getAnnotation().length, 0);
}
}
}
* peptide models for PCA
*/
List<ScoreModelI> filtered = CalculationChooser
- .getApplicableScoreModels(false, true, true,false);
+ .getApplicableScoreModels(false, true, true, false);
assertEquals(filtered.size(), 5);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(4).getName(),
+ "Secondary Structure Similarity");
/*
* peptide models for Tree are the same
*/
- filtered = CalculationChooser.getApplicableScoreModels(false, false, true,false);
+ filtered = CalculationChooser.getApplicableScoreModels(false, false,
+ true, false);
assertEquals(filtered.size(), 5);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(4).getName(),
+ "Secondary Structure Similarity");
/*
* nucleotide models for PCA
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
/*
* nucleotide models for Tree are the same
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, false, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, false,
+ false, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
/*
* nucleotide models for Tree are unchanged
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, false, true,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, false,
+ true, false);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(3).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(3).getName(),
+ "Secondary Structure Similarity");
/*
* nucleotide models for PCA add BLOSUM62 as last option
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, false);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
assertSame(filtered.get(3), blosum62);
-
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,true);
+
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, true);
assertEquals(filtered.size(), 1); // DNA matrix for DNA pasimap
- for (int i=0; i<=8;i++)
+ for (int i = 0; i <= 8; i++)
{
- boolean isDna = (i & 1) != 0,isPca = (i & 2) != 0,isSS = (i & 4) != 0;
-
- assertEquals(CalculationChooser.getApplicableScoreModels(isDna,isPca,isSS,true).size(), (isDna) ? 1: 2);
+ boolean isDna = (i & 1) != 0, isPca = (i & 2) != 0,
+ isSS = (i & 4) != 0;
+
+ assertEquals(CalculationChooser
+ .getApplicableScoreModels(isDna, isPca, isSS, true).size(),
+ (isDna) ? 1 : 2);
}
}
}
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
SecondaryStructureCount secondaryStructureCount)
{
// TODO Auto-generated method stub
-
+
}
@Override
// viewport
// assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
}
+
@Test
public void testDocString()
{
git://source.jalview.org / jalview.git / commitdiff