<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
<classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
<classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
+ <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
<classpathentry kind="output" path="classes"/>
</classpath>
-jalview.release=releases/Release_2_10_3_Branch
-jalview.version=2.10.3b1
+jalview.release=releases/Release_2_10_4_Branch
+jalview.version=2.10.4
To get JSON output instead use:
java -jar target/benchmarks.jar -rf json
+ To run a specific benchmark file use:
+ java -jar target/benchmarks.jar <Benchmark class name>
+
JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
To get help use the standard -h option:
6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again.
+
@Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
@Fork(1)
public class HiddenColumnsBenchmark
-{
- /*
- * State with multiple hidden columns and a start position set
- */
- @State(Scope.Thread)
- public static class HiddenColsAndStartState
- {
- @Param({ "300", "10000", "100000" })
- public int maxcols;
-
- @Param({ "1", "50", "90" })
- public int startpcnt; // position as percentage of maxcols
-
- @Param({ "1", "15", "100" })
- public int hide;
-
- HiddenColumns h = new HiddenColumns();
-
- Random rand = new Random();
-
- public int hiddenColumn;
-
- public int visibleColumn;
-
- @Setup
- public void setup()
+{
+ /*
+ * State with multiple hidden columns and a start position set
+ */
+ @State(Scope.Thread)
+ public static class HiddenColsAndStartState
+ {
+ @Param({"100", "1000", "10000", "100000", "1000000"})
+ public int maxcols;
+
+ @Param({"1", "50", "90"})
+ public int startpcnt; // position as percentage of maxcols
+
+ @Param({"1","15","100"})
+ public int hide;
+
+ HiddenColumns h = new HiddenColumns();
+ Random rand = new Random();
+
+ public int hiddenColumn;
+ public int visibleColumn;
+
+ @Setup
+ public void setup()
+ {
+ rand.setSeed(1234);
+ int lastcol = 0;
+ while (lastcol < maxcols)
+ {
+ int count = rand.nextInt(100);
+ lastcol += count;
+ h.hideColumns(lastcol, lastcol+hide);
+ lastcol+=hide;
+ }
+
+ // make sure column at start is hidden
+ hiddenColumn = (int)(maxcols * startpcnt/100.0);
+ h.hideColumns(hiddenColumn, hiddenColumn);
+
+ // and column <hide> after start is visible
+ ColumnSelection sel = new ColumnSelection();
+ h.revealHiddenColumns(hiddenColumn+hide, sel);
+ visibleColumn = hiddenColumn+hide;
+
+ System.out.println("Maxcols: " + maxcols + " HiddenCol: " + hiddenColumn + " Hide: " + hide);
+ System.out.println("Number of hidden columns: " + h.getSize());
+ }
+ }
+
+ /* Convention: functions in alphabetical order */
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.visibleToAbsoluteColumn(tstate.visibleColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.absoluteToVisibleColumn(tstate.visibleColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchGetSize(HiddenColsAndStartState tstate)
{
- rand.setSeed(1234);
- int lastcol = 0;
- while (lastcol < maxcols)
- {
- int count = rand.nextInt(100);
- lastcol += count;
- h.hideColumns(lastcol, lastcol + hide);
- lastcol += hide;
- }
-
- // make sure column at start is hidden
- hiddenColumn = (int) (maxcols * startpcnt / 100.0);
- h.hideColumns(hiddenColumn, hiddenColumn);
-
- // and column <hide> after start is visible
- ColumnSelection sel = new ColumnSelection();
- h.revealHiddenColumns(hiddenColumn + hide, sel);
- visibleColumn = hiddenColumn + hide;
-
- System.out.println("Maxcols: " + maxcols + " HiddenCol: "
- + hiddenColumn + " Hide: " + hide);
- System.out.println("Number of hidden columns: " + h.getSize());
+ return tstate.h.getSize();
}
- }
-
- /* Convention: functions in alphabetical order */
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
- {
- return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public int benchFindColumnPosition(HiddenColsAndStartState tstate)
- {
- return tstate.h.findColumnPosition(tstate.visibleColumn);
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public List<Integer> benchFindHiddenRegionPositions(
- HiddenColsAndStartState tstate)
- {
- return tstate.h.findHiddenRegionPositions();
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public ArrayList<int[]> benchGetHiddenColumnsCopy(
- HiddenColsAndStartState tstate)
- {
- return tstate.h.getHiddenColumnsCopy();
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public int benchGetSize(HiddenColsAndStartState tstate)
- {
- return tstate.h.getSize();
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
- {
- tstate.h.hideColumns(tstate.visibleColumn, tstate.visibleColumn + 2000);
- return tstate.h;
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public boolean benchIsVisible(HiddenColsAndStartState tstate)
- {
- return tstate.h.isVisible(tstate.hiddenColumn);
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public HiddenColumns benchReveal(HiddenColsAndStartState tstate)
- {
- ColumnSelection sel = new ColumnSelection();
- tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
- return tstate.h;
- }
-
- @Benchmark
- @BenchmarkMode({ Mode.Throughput })
- public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate)
- {
- ColumnSelection sel = new ColumnSelection();
- tstate.h.revealAllHiddenColumns(sel);
- return tstate.h;
- }
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
+ {
+ tstate.h.hideColumns(tstate.visibleColumn,
+ tstate.visibleColumn+2000);
+ return tstate.h;
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public boolean benchIsVisible(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.isVisible(tstate.hiddenColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public HiddenColumns benchReveal(HiddenColsAndStartState tstate)
+ {
+ ColumnSelection sel = new ColumnSelection();
+ tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+ return tstate.h;
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate)
+ {
+ ColumnSelection sel = new ColumnSelection();
+ tstate.h.revealAllHiddenColumns(sel);
+ return tstate.h;
+ }
+
+
}
\ No newline at end of file
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<project name="jalviewX" default="usage" basedir=".">
+<project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+ xmlns:unless="ant:unless">
<target name="help" depends="usage" />
<target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<!-- default TestNG groups to run -->
<property name="testng-groups" value="Functional" />
+ <!-- Java 9 JVM args -->
+ <condition property="java9">
+ <equals arg1="${ant.java.version}" arg2="9"/>
+ </condition>
<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<pathelement location="${testOutputDir}" />
<path refid="test.classpath" />
</classpath>
+ <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
+ <jvmarg value="--illegal-access=warn" if:set="java9"/>
<classfileset dir="${testOutputDir}" includes="**/*.class" />
</testng>
</target>
<exclude name="jalview.jar" />
<include name="*.jar" />
<include name="*_*.jar" />
- <exclude name="*jnilib.jar" />
+ <exclude name="*quaqua*.jar" />
</fileset>
<property name="jalview.version" value="${JALVIEW_VERSION}" />
</resources>
<resources os="Mac OS X">
<fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar" />
+ <include name="quaqua-filechooser-only-8.0.jar"/>
+ <include name="*quaqua64*.jnilib.jar" />
</fileset>
</resources>
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
<copy todir="${outputDir}/lang">
<fileset dir="${resourceDir}/lang">
<include name="MCview/**" />
<include name="jalview/**" />
<include name=".build_properties" />
- <include name="images/idwidth.gif" />
<include name="images/link.gif" />
<include name="lang/**" />
</fileset>
--- /dev/null
+HEADER TRANSFERASE/TRANSFERASE INHIBITOR 01-JAN-13 4IM2
+TITLE STRUCTURE OF TANK-BINDING KINASE 1 (Truncated test file)
+ATOM 3510 N LEU A 468 76.337 90.332 -7.628 1.00168.53 N
+ANISOU 3510 N LEU A 468 19760 15191 29082 5189 1248 -1702 N
+ATOM 3511 CA LEU A 468 75.576 90.788 -6.476 1.00181.60 C
+ANISOU 3511 CA LEU A 468 21073 16927 30998 5158 1421 -2051 C
+ATOM 3512 C LEU A 468 76.285 91.971 -5.836 1.00196.57 C
+ANISOU 3512 C LEU A 468 23029 18636 33021 5053 1667 -2229 C
+ATOM 3513 O LEU A 468 75.727 93.067 -5.733 1.00197.97 O
+ANISOU 3513 O LEU A 468 23115 18581 33523 5166 1662 -2304 O
+ATOM 3514 CB LEU A 468 75.409 89.671 -5.449 1.00173.72 C
+ANISOU 3514 CB LEU A 468 19829 16340 29836 4981 1593 -2304 C
+ATOM 3515 CG LEU A 468 74.099 88.882 -5.420 1.00170.58 C
+ANISOU 3515 CG LEU A 468 19142 16142 29529 5074 1449 -2345 C
+ATOM 3516 CD1 LEU A 468 74.023 87.940 -6.581 1.00167.98 C
+ANISOU 3516 CD1 LEU A 468 18951 15858 29015 5180 1156 -2025 C
+ATOM 3517 CD2 LEU A 468 73.988 88.096 -4.145 1.00165.16 C
+ANISOU 3517 CD2 LEU A 468 18217 15818 28720 4865 1706 -2656 C
+ATOM 3518 N ASP A 469 77.529 91.753 -5.429 1.00208.80 N
+ANISOU 3518 N ASP A 469 24731 20282 34322 4836 1875 -2296 N
+ATOM 3519 CA ASP A 469 78.267 92.785 -4.720 1.00223.11 C
+ANISOU 3519 CA ASP A 469 26577 21960 36233 4701 2123 -2500 C
+ATOM 3520 C ASP A 469 78.653 93.973 -5.599 1.00231.96 C
+ANISOU 3520 C ASP A 469 27954 22654 37525 4817 2037 -2283 C
+ATOM 3521 O ASP A 469 78.718 95.100 -5.118 1.00235.71 O
+ANISOU 3521 O ASP A 469 28377 22940 38242 4798 2175 -2449 O
+ATOM 3522 CB ASP A 469 79.506 92.197 -4.057 1.00224.50 C
+ANISOU 3522 CB ASP A 469 26841 22370 36089 4433 2350 -2633 C
+ATOM 3523 CG ASP A 469 79.748 92.767 -2.679 1.00229.51 C
+ANISOU 3523 CG ASP A 469 27303 23107 36794 4254 2637 -3018 C
+ATOM 3524 OD1 ASP A 469 79.958 93.992 -2.564 1.00232.36 O
+ANISOU 3524 OD1 ASP A 469 27695 23203 37387 4262 2718 -3093 O
+ATOM 3525 OD2 ASP A 469 79.751 91.979 -1.709 1.00229.48 O
+ANISOU 3525 OD2 ASP A 469 27145 23450 36598 4098 2779 -3242 O
+ATOM 3526 N PHE A 470 78.904 93.735 -6.882 1.00233.88 N
+ANISOU 3526 N PHE A 470 28481 22742 37641 4931 1813 -1912 N
+ATOM 3527 CA PHE A 470 79.292 94.831 -7.766 1.00237.73 C
+ANISOU 3527 CA PHE A 470 29252 22819 38256 5033 1733 -1677 C
+ATOM 3528 C PHE A 470 78.103 95.470 -8.467 1.00232.15 C
+ANISOU 3528 C PHE A 470 28512 21868 37828 5322 1470 -1512 C
+ATOM 3529 O PHE A 470 78.021 96.691 -8.532 1.00230.69 O
+ANISOU 3529 O PHE A 470 28371 21372 37909 5402 1493 -1517 O
+ATOM 3530 CB PHE A 470 80.344 94.379 -8.784 1.00242.99 C
+ANISOU 3530 CB PHE A 470 30297 23410 38616 4976 1661 -1357 C
+ATOM 3531 CG PHE A 470 80.663 95.388 -9.839 1.00251.53 C
+ANISOU 3531 CG PHE A 470 31709 24074 39788 5089 1550 -1064 C
+ATOM 3532 CD1 PHE A 470 81.658 96.315 -9.620 1.00252.90 C
+ANISOU 3532 CD1 PHE A 470 32021 24036 40032 4942 1771 -1133 C
+ATOM 3533 CD2 PHE A 470 80.005 95.389 -11.059 1.00255.02 C
+ANISOU 3533 CD2 PHE A 470 32335 24339 40221 5330 1225 -715 C
+ATOM 3534 CE1 PHE A 470 81.981 97.242 -10.575 1.00254.75 C
+ANISOU 3534 CE1 PHE A 470 32569 23879 40344 5028 1688 -862 C
+ATOM 3535 CE2 PHE A 470 80.321 96.320 -12.027 1.00256.76 C
+ANISOU 3535 CE2 PHE A 470 32894 24173 40491 5427 1126 -433 C
+ATOM 3536 CZ PHE A 470 81.313 97.248 -11.784 1.00256.57 C
+ANISOU 3536 CZ PHE A 470 33006 23929 40550 5272 1365 -504 C
+ATOM 3537 N CYS A 471 77.190 94.665 -8.997 1.00176.88 N
+ANISOU 3537 N CYS A 471 20955 21812 24441 2225 -3821 -3711 N
+ATOM 3538 CA CYS A 471 76.124 95.233 -9.815 1.00176.41 C
+ANISOU 3538 CA CYS A 471 20820 21906 24301 2124 -3576 -3614 C
+ATOM 3539 C CYS A 471 74.868 95.631 -9.050 1.00176.82 C
+ANISOU 3539 C CYS A 471 21026 22206 23952 2247 -3588 -3734 C
+ATOM 3540 O CYS A 471 74.632 96.811 -8.854 1.00178.66 O
+ANISOU 3540 O CYS A 471 21175 22393 24314 2353 -3749 -3873 O
+ATOM 3541 CB CYS A 471 75.805 94.346 -11.019 1.00173.95 C
+ANISOU 3541 CB CYS A 471 20521 21694 23877 1925 -3217 -3359 C
+ATOM 3542 SG CYS A 471 76.954 94.571 -12.398 1.00273.04 S
+ANISOU 3542 SG CYS A 471 32850 33934 36957 1863 -3075 -3146 S
+ATOM 3543 N ILE A 472 74.068 94.670 -8.603 1.00173.50 N
+ANISOU 3543 N ILE A 472 20813 22023 23085 2253 -3402 -3662 N
+ATOM 3544 CA ILE A 472 72.771 95.033 -8.022 1.00171.09 C
+ANISOU 3544 CA ILE A 472 20616 21936 22453 2374 -3307 -3694 C
+ATOM 3545 C ILE A 472 72.832 96.022 -6.874 1.00177.82 C
+ANISOU 3545 C ILE A 472 21591 22750 23222 2698 -3611 -3931 C
+ATOM 3546 O ILE A 472 71.992 96.914 -6.776 1.00182.92 O
+ANISOU 3546 O ILE A 472 22220 23491 23792 2778 -3598 -3985 O
+ATOM 3547 CB ILE A 472 71.979 93.843 -7.518 1.00159.41 C
+ANISOU 3547 CB ILE A 472 19318 20653 20599 2393 -3038 -3546 C
+ATOM 3548 CG1 ILE A 472 70.708 93.667 -8.341 1.00147.27 C
+ANISOU 3548 CG1 ILE A 472 17653 19253 19051 2196 -2745 -3384 C
+ATOM 3549 CG2 ILE A 472 71.526 94.090 -6.105 1.00155.95 C
+ANISOU 3549 CG2 ILE A 472 19129 20312 19812 2752 -3085 -3637 C
+ATOM 3550 CD1 ILE A 472 70.927 92.915 -9.606 1.00135.92 C
+ANISOU 3550 CD1 ILE A 472 16097 17752 17794 1929 -2643 -3254 C
+ATOM 3551 N ARG A 473 73.812 95.865 -5.996 1.00180.33 N
+ANISOU 3551 N ARG A 473 22055 22917 23544 2920 -3920 -4092 N
+ATOM 3552 CA ARG A 473 73.860 96.762 -4.877 1.00189.65 C
+ANISOU 3552 CA ARG A 473 23415 24034 24610 3307 -4283 -4357 C
+ATOM 3553 C ARG A 473 74.328 98.021 -5.558 1.00185.98 C
+ANISOU 3553 C ARG A 473 22628 23344 24692 3195 -4530 -4477 C
+ATOM 3554 O ARG A 473 73.519 98.885 -5.866 1.00181.76 O
+ANISOU 3554 O ARG A 473 22002 22904 24153 3165 -4446 -4474 O
+ATOM 3555 CB ARG A 473 74.803 96.287 -3.768 1.00205.24 C
+ANISOU 3555 CB ARG A 473 25661 25862 26460 3635 -4629 -4545 C
+ATOM 3556 CG ARG A 473 74.468 96.921 -2.433 1.00220.50 C
+ANISOU 3556 CG ARG A 473 27955 27814 28011 4171 -4923 -4787 C
+ATOM 3557 CD ARG A 473 75.337 96.433 -1.295 1.00232.58 C
+ANISOU 3557 CD ARG A 473 29837 29192 29341 4591 -5300 -5003 C
+ATOM 3558 NE ARG A 473 76.763 96.602 -1.549 1.00237.46 N
+ANISOU 3558 NE ARG A 473 30220 29440 30564 4489 -5773 -5205 N
+ATOM 3559 CZ ARG A 473 77.716 95.991 -0.861 1.00240.32 C
+ANISOU 3559 CZ ARG A 473 30786 29623 30903 4725 -6098 -5371 C
+ATOM 3560 NH1 ARG A 473 77.388 95.172 0.115 1.00241.12 N
+ANISOU 3560 NH1 ARG A 473 31370 29900 30344 5100 -5978 -5355 N
+ATOM 3561 NH2 ARG A 473 78.988 96.195 -1.159 1.00241.54 N
+ANISOU 3561 NH2 ARG A 473 30651 29398 31724 4605 -6518 -5533 N
+ATOM 3562 N ASN A 474 75.608 98.073 -5.901 1.00188.74 N
+ANISOU 3562 N ASN A 474 22768 23381 25563 3107 -4772 -4534 N
+ATOM 3563 CA ASN A 474 76.168 99.264 -6.526 1.00188.61 C
+ANISOU 3563 CA ASN A 474 22395 23075 26194 3026 -4977 -4605 C
+ATOM 3564 C ASN A 474 75.420 99.892 -7.729 1.00173.98 C
+ANISOU 3564 C ASN A 474 20312 21326 24467 2781 -4623 -4414 C
+ATOM 3565 O ASN A 474 75.482 101.107 -7.891 1.00176.08 O
+ANISOU 3565 O ASN A 474 20374 21426 25104 2827 -4803 -4518 O
+ATOM 3566 CB ASN A 474 77.650 99.066 -6.857 1.00199.45 C
+ANISOU 3566 CB ASN A 474 23514 24060 28207 2939 -5170 -4595 C
+ATOM 3567 CG ASN A 474 78.504 98.809 -5.625 1.00210.23 C
+ANISOU 3567 CG ASN A 474 25062 25219 29597 3243 -5689 -4883 C
+ATOM 3568 OD1 ASN A 474 78.174 99.240 -4.527 1.00215.26 O
+ANISOU 3568 OD1 ASN A 474 25969 25891 29928 3596 -6043 -5160 O
+ATOM 3569 ND2 ASN A 474 79.613 98.103 -5.810 1.00212.07 N
+ANISOU 3569 ND2 ASN A 474 25176 25222 30179 3148 -5748 -4822 N
+ATOM 3570 N ILE A 475 74.722 99.114 -8.562 1.00161.86 N
+ANISOU 3570 N ILE A 475 18813 20033 22652 2556 -4165 -4158 N
+ATOM 3571 CA ILE A 475 74.022 99.727 -9.709 1.00154.84 C
+ANISOU 3571 CA ILE A 475 17755 19216 21861 2390 -3885 -4015 C
+ATOM 3572 C ILE A 475 72.785 100.520 -9.312 1.00159.27 C
+ANISOU 3572 C ILE A 475 18401 19995 22121 2490 -3891 -4125 C
+ATOM 3573 O ILE A 475 72.662 101.687 -9.663 1.00162.60 O
+ANISOU 3573 O ILE A 475 18651 20327 22804 2505 -3962 -4186 O
+ATOM 3574 CB ILE A 475 73.600 98.727 -10.818 1.00214.93 C
+ANISOU 3574 CB ILE A 475 25397 26975 29293 2173 -3475 -3753 C
+ATOM 3575 CG1 ILE A 475 74.808 98.227 -11.613 1.00218.74 C
+ANISOU 3575 CG1 ILE A 475 25753 27211 30145 2083 -3390 -3585 C
+ATOM 3576 CG2 ILE A 475 72.618 99.379 -11.789 1.00210.37 C
+ANISOU 3576 CG2 ILE A 475 24743 26509 28681 2097 -3256 -3677 C
+ATOM 3577 CD1 ILE A 475 74.446 97.201 -12.664 1.00218.15 C
+ANISOU 3577 CD1 ILE A 475 25777 27260 29850 1946 -3056 -3359 C
+ATOM 3578 N GLU A 476 71.856 99.893 -8.600 1.00156.45 N
+ANISOU 3578 N GLU A 476 18293 19907 21245 2571 -3778 -4120 N
+ATOM 3579 CA GLU A 476 70.623 100.594 -8.252 1.00142.72 C
+ANISOU 3579 CA GLU A 476 16627 18370 19231 2677 -3720 -4176 C
+ATOM 3580 C GLU A 476 70.845 101.560 -7.094 1.00144.41 C
+ANISOU 3580 C GLU A 476 16959 18500 19412 3012 -4114 -4440 C
+ATOM 3581 O GLU A 476 70.012 102.417 -6.811 1.00142.58 O
+ANISOU 3581 O GLU A 476 16768 18380 19024 3141 -4136 -4517 O
+ATOM 3582 CB GLU A 476 69.486 99.616 -7.958 1.00128.68 C
+ANISOU 3582 CB GLU A 476 15020 16860 17012 2665 -3395 -4018 C
+ATOM 3583 CG GLU A 476 69.562 98.905 -6.628 1.00128.73 C
+ANISOU 3583 CG GLU A 476 15321 16930 16662 2941 -3433 -4041 C
+ATOM 3584 CD GLU A 476 68.465 97.866 -6.484 1.00133.35 C
+ANISOU 3584 CD GLU A 476 15992 17719 16955 2900 -3026 -3806 C
+ATOM 3585 OE1 GLU A 476 68.285 97.061 -7.422 1.00132.30 O
+ANISOU 3585 OE1 GLU A 476 15710 17598 16962 2603 -2816 -3643 O
+ATOM 3586 OE2 GLU A 476 67.768 97.860 -5.448 1.00136.37 O
+ANISOU 3586 OE2 GLU A 476 16588 18223 17003 3196 -2912 -3773 O
+ATOM 3587 N LYS A 477 71.990 101.424 -6.439 1.00148.46 N
+ANISOU 3587 N LYS A 477 17534 18788 20087 3179 -4467 -4596 N
+ATOM 3588 CA LYS A 477 72.399 102.365 -5.405 1.00154.25 C
+ANISOU 3588 CA LYS A 477 18378 19348 20882 3544 -4976 -4907 C
+ATOM 3589 C LYS A 477 72.634 103.732 -5.994 1.00159.76 C
+ANISOU 3589 C LYS A 477 18754 19833 22117 3467 -5183 -5014 C
+ATOM 3590 O LYS A 477 72.568 104.742 -5.292 1.00158.01 O
+ANISOU 3590 O LYS A 477 18598 19516 21921 3749 -5568 -5266 O
+ATOM 3591 CB LYS A 477 73.667 101.883 -4.706 1.00154.03 C
+ANISOU 3591 CB LYS A 477 18446 19057 21022 3730 -5372 -5076 C
+ATOM 3592 CG LYS A 477 73.367 100.787 -3.750 1.00149.76 C
+ANISOU 3592 CG LYS A 477 18324 18717 19861 3975 -5258 -5042 C
+ATOM 3593 CD LYS A 477 74.437 100.554 -2.740 1.00143.39 C
+ANISOU 3593 CD LYS A 477 17737 17664 19082 4327 -5762 -5306 C
+ATOM 3594 CE LYS A 477 73.739 100.087 -1.488 1.00145.72 C
+ANISOU 3594 CE LYS A 477 18569 18186 18613 4805 -5697 -5337 C
+ATOM 3595 NZ LYS A 477 74.661 99.556 -0.469 1.00149.42 N
+ANISOU 3595 NZ LYS A 477 19366 18470 18936 5206 -6108 -5561 N
+ATOM 3596 N THR A 478 72.908 103.757 -7.293 1.00166.45 N
+ANISOU 3596 N THR A 478 19271 20589 23384 3124 -4918 -4810 N
+ATOM 3597 CA THR A 478 73.186 105.012 -7.968 1.00170.99 C
+ANISOU 3597 CA THR A 478 19509 20929 24531 3052 -5023 -4844 C
+ATOM 3598 C THR A 478 71.905 105.733 -8.391 1.00172.33 C
+ANISOU 3598 C THR A 478 19686 21358 24435 2999 -4780 -4796 C
+ATOM 3599 O THR A 478 71.021 105.170 -9.046 1.00163.10 O
+ANISOU 3599 O THR A 478 18581 20461 22928 2823 -4356 -4594 O
+ATOM 3600 CB THR A 478 74.217 104.856 -9.128 1.00146.93 C
+ANISOU 3600 CB THR A 478 16115 17589 22125 2815 -4843 -4626 C
+ATOM 3601 OG1 THR A 478 74.873 106.106 -9.369 1.00147.15 O
+ANISOU 3601 OG1 THR A 478 15790 17239 22881 2857 -5085 -4705 O
+ATOM 3602 CG2 THR A 478 73.562 104.391 -10.425 1.00144.32 C
+ANISOU 3602 CG2 THR A 478 15764 17473 21597 2570 -4282 -4318 C
+ATOM 3603 N VAL A 479 71.809 106.979 -7.944 1.00177.73 N
+ANISOU 3603 N VAL A 479 20309 21929 25291 3181 -5110 -5014 N
+ATOM 3604 CA VAL A 479 70.674 107.838 -8.218 1.00175.65 C
+ANISOU 3604 CA VAL A 479 20044 21875 24819 3171 -4959 -5013 C
+ATOM 3605 C VAL A 479 71.176 109.077 -8.939 1.00177.67 C
+ANISOU 3605 C VAL A 479 19928 21830 25749 3101 -5069 -5035 C
+ATOM 3606 O VAL A 479 72.353 109.417 -8.840 1.00179.02 O
+ANISOU 3606 O VAL A 479 19865 21600 26555 3150 -5387 -5121 O
+ATOM 3607 CB VAL A 479 69.983 108.266 -6.909 1.00168.37 C
+ANISOU 3607 CB VAL A 479 19442 21113 23418 3524 -5243 -5249 C
+ATOM 3608 CG1 VAL A 479 69.008 109.403 -7.169 1.00162.23 C
+ANISOU 3608 CG1 VAL A 479 18603 20470 22565 3531 -5176 -5285 C
+ATOM 3609 CG2 VAL A 479 69.288 107.080 -6.256 1.00163.89 C
+ANISOU 3609 CG2 VAL A 479 19236 20856 22180 3624 -4991 -5142 C
+ATOM 3610 N MET A 486 57.931 103.433 -6.150 1.00 92.00 N
+ANISOU 3610 N MET A 486 10154 13425 11375 3371 -1523 -3283 N
+ATOM 3611 CA MET A 486 56.824 104.104 -5.482 1.00110.61 C
+ANISOU 3611 CA MET A 486 12558 15882 13585 3644 -1287 -3161 C
+ATOM 3612 C MET A 486 56.182 105.150 -6.389 1.00111.38 C
+ANISOU 3612 C MET A 486 12428 16016 13877 3424 -1416 -3308 C
+ATOM 3613 O MET A 486 56.000 106.305 -6.002 1.00120.35 O
+ANISOU 3613 O MET A 486 13691 17243 14794 3639 -1526 -3430 O
+ATOM 3614 CB MET A 486 57.288 104.743 -4.170 1.00120.60 C
+ANISOU 3614 CB MET A 486 14253 17221 14347 4174 -1395 -3243 C
+ATOM 3615 CG MET A 486 58.405 105.768 -4.316 1.00126.87 C
+ANISOU 3615 CG MET A 486 15171 17987 15047 4196 -1944 -3629 C
+ATOM 3616 SD MET A 486 58.150 107.169 -3.210 1.00146.78 S
+ANISOU 3616 SD MET A 486 18044 20597 17128 4757 -2124 -3782 S
+ATOM 3617 CE MET A 486 58.003 106.326 -1.640 1.00102.35 C
+ANISOU 3617 CE MET A 486 12883 15002 11003 5391 -1797 -3524 C
+ATOM 3618 N GLY A 496 57.154 99.412 -2.065 1.00157.62 N
+ANISOU 3618 N GLY A 496 19150 21656 19083 4616 82 -2024 N
+ATOM 3619 CA GLY A 496 57.031 99.217 -3.498 1.00158.07 C
+ANISOU 3619 CA GLY A 496 18749 21636 19677 3991 -116 -2141 C
+ATOM 3620 C GLY A 496 57.664 97.914 -3.942 1.00163.71 C
+ANISOU 3620 C GLY A 496 19349 22235 20619 3709 -140 -2093 C
+ATOM 3621 O GLY A 496 58.040 97.090 -3.111 1.00167.17 O
+ANISOU 3621 O GLY A 496 20009 22652 20858 3970 79 -1915 O
+ATOM 3622 N GLU A 497 57.778 97.722 -5.254 1.00166.67 N
+ANISOU 3622 N GLU A 497 19413 22530 21383 3222 -403 -2250 N
+ATOM 3623 CA GLU A 497 58.431 96.534 -5.792 1.00170.73 C
+ANISOU 3623 CA GLU A 497 19840 22933 22098 2955 -485 -2239 C
+ATOM 3624 C GLU A 497 59.931 96.621 -5.556 1.00172.64 C
+ANISOU 3624 C GLU A 497 20403 23228 21965 3043 -809 -2472 C
+ATOM 3625 O GLU A 497 60.589 95.609 -5.311 1.00173.01 O
+ANISOU 3625 O GLU A 497 20547 23223 21965 3047 -764 -2395 O
+ATOM 3626 CB GLU A 497 58.173 96.394 -7.290 1.00169.62 C
+ANISOU 3626 CB GLU A 497 19361 22681 22408 2505 -727 -2374 C
+ATOM 3627 CG GLU A 497 56.882 97.012 -7.777 1.00173.11 C
+ANISOU 3627 CG GLU A 497 19518 23086 23171 2413 -663 -2350 C
+ATOM 3628 CD GLU A 497 56.703 96.840 -9.270 1.00173.61 C
+ANISOU 3628 CD GLU A 497 19329 23013 23621 2054 -974 -2531 C
+ATOM 3629 OE1 GLU A 497 57.597 96.241 -9.908 1.00170.78 O
+ANISOU 3629 OE1 GLU A 497 19040 22600 23250 1901 -1202 -2647 O
+ATOM 3630 OE2 GLU A 497 55.672 97.300 -9.805 1.00174.73 O
+ANISOU 3630 OE2 GLU A 497 19233 23093 24064 1967 -999 -2559 O
+ATOM 3631 N ILE A 498 60.466 97.836 -5.652 1.00171.44 N
+ANISOU 3631 N ILE A 498 20381 23149 21608 3107 -1147 -2757 N
+ATOM 3632 CA ILE A 498 61.883 98.078 -5.403 1.00167.93 C
+ANISOU 3632 CA ILE A 498 20186 22695 20926 3210 -1503 -2995 C
+ATOM 3633 C ILE A 498 62.251 97.620 -4.004 1.00173.82 C
+ANISOU 3633 C ILE A 498 21298 23465 21280 3659 -1379 -2903 C
+ATOM 3634 O ILE A 498 63.315 97.034 -3.789 1.00168.12 O
+ANISOU 3634 O ILE A 498 20732 22684 20462 3692 -1544 -2980 O
+ATOM 3635 CB ILE A 498 62.227 99.564 -5.520 1.00165.53 C
+ANISOU 3635 CB ILE A 498 19934 22420 20540 3287 -1855 -3283 C
+ATOM 3636 CG1 ILE A 498 61.848 100.100 -6.901 1.00171.37 C
+ANISOU 3636 CG1 ILE A 498 20360 23137 21618 2911 -1947 -3365 C
+ATOM 3637 CG2 ILE A 498 63.706 99.798 -5.239 1.00153.61 C
+ANISOU 3637 CG2 ILE A 498 18613 20820 18931 3398 -2256 -3525 C
+ATOM 3638 CD1 ILE A 498 61.891 101.605 -6.996 1.00174.73 C
+ANISOU 3638 CD1 ILE A 498 20793 23594 22004 2996 -2195 -3587 C
+ATOM 3639 N SER A 499 61.362 97.890 -3.054 1.00187.32 N
+ANISOU 3639 N SER A 499 23169 25252 22753 4049 -1074 -2727 N
+ATOM 3640 CA SER A 499 61.558 97.444 -1.683 1.00198.47 C
+ANISOU 3640 CA SER A 499 24999 26682 23729 4594 -880 -2593 C
+ATOM 3641 C SER A 499 61.611 95.926 -1.651 1.00206.95 C
+ANISOU 3641 C SER A 499 26003 27687 24943 4481 -548 -2315 C
+ATOM 3642 O SER A 499 62.302 95.334 -0.823 1.00211.11 O
+ANISOU 3642 O SER A 499 26867 28195 25151 4806 -533 -2293 O
+ATOM 3643 CB SER A 499 60.435 97.952 -0.780 1.00200.16 C
+ANISOU 3643 CB SER A 499 25385 26976 23690 5064 -498 -2368 C
+ATOM 3644 OG SER A 499 60.635 97.541 0.556 1.00203.12 O
+ANISOU 3644 OG SER A 499 26244 27359 23574 5697 -286 -2224 O
+ATOM 3645 N ASP A 500 60.877 95.300 -2.564 1.00209.43 N
+ANISOU 3645 N ASP A 500 25883 27938 25751 4040 -320 -2123 N
+ATOM 3646 CA ASP A 500 60.862 93.851 -2.655 1.00212.36 C
+ANISOU 3646 CA ASP A 500 26120 28207 26361 3883 -39 -1865 C
+ATOM 3647 C ASP A 500 62.097 93.307 -3.366 1.00203.21 C
+ANISOU 3647 C ASP A 500 24946 26999 25265 3557 -426 -2093 C
+ATOM 3648 O ASP A 500 62.511 92.195 -3.092 1.00204.96 O
+ANISOU 3648 O ASP A 500 25238 27165 25472 3573 -286 -1954 O
+ATOM 3649 CB ASP A 500 59.580 93.355 -3.335 1.00221.23 C
+ANISOU 3649 CB ASP A 500 26765 29217 28075 3573 287 -1593 C
+ATOM 3650 CG ASP A 500 58.346 93.583 -2.486 1.00233.55 C
+ANISOU 3650 CG ASP A 500 28310 30773 29657 3938 816 -1243 C
+ATOM 3651 OD1 ASP A 500 58.502 93.807 -1.272 1.00239.09 O
+ANISOU 3651 OD1 ASP A 500 29432 31558 29852 4492 1029 -1137 O
+ATOM 3652 OD2 ASP A 500 57.226 93.532 -3.034 1.00237.24 O
+ANISOU 3652 OD2 ASP A 500 28355 31128 30656 3709 1011 -1072 O
+ATOM 3653 N ILE A 501 62.692 94.094 -4.258 1.00192.67 N
+ANISOU 3653 N ILE A 501 23525 25673 24008 3292 -875 -2413 N
+ATOM 3654 CA ILE A 501 63.864 93.633 -5.007 1.00181.71 C
+ANISOU 3654 CA ILE A 501 22108 24215 22719 3006 -1195 -2587 C
+ATOM 3655 C ILE A 501 65.165 93.699 -4.196 1.00170.68 C
+ANISOU 3655 C ILE A 501 21064 22814 20972 3287 -1450 -2764 C
+ATOM 3656 O ILE A 501 65.940 92.735 -4.173 1.00164.70 O
+ANISOU 3656 O ILE A 501 20376 21999 20202 3222 -1476 -2736 O
+ATOM 3657 CB ILE A 501 64.023 94.385 -6.353 1.00138.03 C
+ANISOU 3657 CB ILE A 501 16341 18649 17453 2657 -1507 -2802 C
+ATOM 3658 CG1 ILE A 501 63.385 93.589 -7.491 1.00130.33 C
+ANISOU 3658 CG1 ILE A 501 15061 17587 16872 2296 -1411 -2683 C
+ATOM 3659 CG2 ILE A 501 65.491 94.642 -6.682 1.00137.98 C
+ANISOU 3659 CG2 ILE A 501 16437 18581 17410 2596 -1883 -3037 C
+ATOM 3660 CD1 ILE A 501 61.877 93.516 -7.426 1.00127.50 C
+ANISOU 3660 CD1 ILE A 501 14480 17217 16748 2292 -1111 -2482 C
+ATOM 3661 N HIS A 502 65.396 94.829 -3.532 1.00164.00 N
+ANISOU 3661 N HIS A 502 20439 22007 19869 3613 -1676 -2964 N
+ATOM 3662 CA HIS A 502 66.603 95.022 -2.737 1.00157.69 C
+ANISOU 3662 CA HIS A 502 19968 21147 18800 3931 -2029 -3195 C
+ATOM 3663 C HIS A 502 66.627 94.018 -1.594 1.00162.64 C
+ANISOU 3663 C HIS A 502 20933 21795 19069 4322 -1761 -3012 C
+ATOM 3664 O HIS A 502 67.677 93.496 -1.229 1.00164.35 O
+ANISOU 3664 O HIS A 502 21348 21935 19163 4433 -1971 -3125 O
+ATOM 3665 CB HIS A 502 66.654 96.452 -2.195 1.00150.83 C
+ANISOU 3665 CB HIS A 502 19272 20282 17755 4264 -2351 -3452 C
+ATOM 3666 CG HIS A 502 67.989 97.117 -2.348 1.00143.78 C
+ANISOU 3666 CG HIS A 502 18387 19223 17019 4248 -2929 -3804 C
+ATOM 3667 ND1 HIS A 502 68.672 97.155 -3.544 1.00137.00 N
+ANISOU 3667 ND1 HIS A 502 17193 18253 16609 3785 -3096 -3872 N
+ATOM 3668 CD2 HIS A 502 68.759 97.787 -1.457 1.00140.15 C
+ANISOU 3668 CD2 HIS A 502 18217 18647 16387 4674 -3387 -4099 C
+ATOM 3669 CE1 HIS A 502 69.807 97.814 -3.383 1.00131.33 C
+ANISOU 3669 CE1 HIS A 502 16503 17343 16055 3893 -3583 -4155 C
+ATOM 3670 NE2 HIS A 502 69.883 98.208 -2.125 1.00130.34 N
+ANISOU 3670 NE2 HIS A 502 16741 17200 15583 4416 -3815 -4326 N
+ATOM 3671 N THR A 503 65.450 93.751 -1.039 1.00163.37 N
+ANISOU 3671 N THR A 503 21080 21971 19022 4552 -1268 -2705 N
+ATOM 3672 CA THR A 503 65.295 92.771 0.033 1.00163.31 C
+ANISOU 3672 CA THR A 503 21384 21972 18696 4974 -872 -2437 C
+ATOM 3673 C THR A 503 65.393 91.327 -0.475 1.00151.49 C
+ANISOU 3673 C THR A 503 19659 20415 17484 4610 -614 -2206 C
+ATOM 3674 O THR A 503 65.955 90.464 0.198 1.00146.11 O
+ANISOU 3674 O THR A 503 19247 19705 16563 4853 -520 -2130 O
+ATOM 3675 CB THR A 503 63.956 92.972 0.783 1.00170.09 C
+ANISOU 3675 CB THR A 503 22342 22899 19387 5379 -334 -2106 C
+ATOM 3676 OG1 THR A 503 64.026 94.162 1.576 1.00176.61 O
+ANISOU 3676 OG1 THR A 503 23551 23775 19778 5902 -585 -2325 O
+ATOM 3677 CG2 THR A 503 63.645 91.790 1.693 1.00171.53 C
+ANISOU 3677 CG2 THR A 503 22747 23054 19374 5760 235 -1707 C
+ATOM 3678 N LYS A 504 64.865 91.071 -1.669 1.00141.41 N
+ANISOU 3678 N LYS A 504 17911 19106 16711 4058 -541 -2117 N
+ATOM 3679 CA LYS A 504 64.918 89.730 -2.251 1.00138.96 C
+ANISOU 3679 CA LYS A 504 17368 18711 16719 3706 -369 -1930 C
+ATOM 3680 C LYS A 504 66.335 89.382 -2.646 1.00142.04 C
+ANISOU 3680 C LYS A 504 17848 19062 17058 3520 -779 -2178 C
+ATOM 3681 O LYS A 504 66.762 88.230 -2.559 1.00134.46 O
+ANISOU 3681 O LYS A 504 16927 18053 16108 3463 -666 -2057 O
+ATOM 3682 CB LYS A 504 64.010 89.614 -3.477 1.00129.82 C
+ANISOU 3682 CB LYS A 504 15721 17488 16116 3223 -303 -1839 C
+ATOM 3683 CG LYS A 504 62.585 89.222 -3.164 1.00130.75 C
+ANISOU 3683 CG LYS A 504 15616 17544 16518 3307 225 -1458 C
+ATOM 3684 N LEU A 505 67.053 90.395 -3.100 1.00138.41 N
+ANISOU 3684 N LEU A 505 17394 18602 16593 3427 -1237 -2505 N
+ATOM 3685 CA LEU A 505 68.435 90.224 -3.458 1.00120.29 C
+ANISOU 3685 CA LEU A 505 15154 16230 14322 3285 -1619 -2726 C
+ATOM 3686 C LEU A 505 69.260 89.889 -2.223 1.00124.70 C
+ANISOU 3686 C LEU A 505 16126 16770 14484 3724 -1710 -2800 C
+ATOM 3687 O LEU A 505 70.166 89.052 -2.259 1.00124.02 O
+ANISOU 3687 O LEU A 505 16106 16619 14396 3643 -1808 -2823 O
+ATOM 3688 CB LEU A 505 68.966 91.499 -4.066 1.00109.42 C
+ANISOU 3688 CB LEU A 505 13673 14807 13094 3171 -2036 -3016 C
+ATOM 3689 CG LEU A 505 70.386 91.097 -4.404 1.00128.61 C
+ANISOU 3689 CG LEU A 505 16120 17111 15635 3034 -2336 -3157 C
+ATOM 3690 CD1 LEU A 505 70.509 91.048 -5.920 1.00141.22 C
+ANISOU 3690 CD1 LEU A 505 17393 18648 17616 2580 -2370 -3131 C
+ATOM 3691 CD2 LEU A 505 71.441 91.946 -3.655 1.00114.58 C
+ANISOU 3691 CD2 LEU A 505 14554 15224 13758 3350 -2784 -3462 C
+ATOM 3692 N LEU A 506 68.951 90.579 -1.132 1.00130.40 N
+ANISOU 3692 N LEU A 506 17159 17539 14847 4233 -1705 -2854 N
+ATOM 3693 CA LEU A 506 69.612 90.336 0.139 1.00131.63 C
+ANISOU 3693 CA LEU A 506 17798 17665 14549 4786 -1814 -2947 C
+ATOM 3694 C LEU A 506 69.501 88.865 0.507 1.00144.65 C
+ANISOU 3694 C LEU A 506 19548 19330 16080 4841 -1380 -2638 C
+ATOM 3695 O LEU A 506 70.448 88.287 1.024 1.00156.36 O
+ANISOU 3695 O LEU A 506 21304 20754 17351 5038 -1550 -2741 O
+ATOM 3696 CB LEU A 506 69.008 91.206 1.240 1.00120.17 C
+ANISOU 3696 CB LEU A 506 16713 16270 12675 5409 -1772 -2980 C
+ATOM 3697 N ARG A 507 68.351 88.260 0.214 1.00146.01 N
+ANISOU 3697 N ARG A 507 19470 19552 16453 4658 -839 -2263 N
+ATOM 3698 CA ARG A 507 68.159 86.831 0.443 1.00152.26 C
+ANISOU 3698 CA ARG A 507 20261 20320 17271 4649 -394 -1930 C
+ATOM 3699 C ARG A 507 69.164 86.004 -0.360 1.00145.14 C
+ANISOU 3699 C ARG A 507 19199 19352 16597 4200 -653 -2042 C
+ATOM 3700 O ARG A 507 69.471 84.873 0.007 1.00142.95 O
+ANISOU 3700 O ARG A 507 19044 19045 16224 4273 -450 -1882 O
+ATOM 3701 CB ARG A 507 66.724 86.401 0.111 1.00161.16 C
+ANISOU 3701 CB ARG A 507 21023 21434 18777 4463 165 -1523 C
+ATOM 3702 CG ARG A 507 65.661 86.975 1.046 1.00177.63 C
+ANISOU 3702 CG ARG A 507 23283 23565 20645 4978 585 -1290 C
+ATOM 3703 CD ARG A 507 64.263 86.468 0.696 1.00187.68 C
+ANISOU 3703 CD ARG A 507 24111 24757 22442 4769 1148 -857 C
+ATOM 3704 NE ARG A 507 63.229 87.082 1.527 1.00198.88 N
+ANISOU 3704 NE ARG A 507 25661 26202 23704 5259 1588 -600 N
+ATOM 3705 CZ ARG A 507 61.923 86.883 1.368 1.00205.71 C
+ANISOU 3705 CZ ARG A 507 26137 26967 25058 5169 2095 -210 C
+ATOM 3706 NH1 ARG A 507 61.484 86.084 0.406 1.00207.33 N
+ANISOU 3706 NH1 ARG A 507 25797 27020 25959 4610 2159 -75 N
+ATOM 3707 NH2 ARG A 507 61.055 87.485 2.171 1.00208.11 N
+ANISOU 3707 NH2 ARG A 507 26596 27293 25185 5668 2517 41 N
+ATOM 3708 N LEU A 508 69.681 86.579 -1.445 1.00134.19 N
+ANISOU 3708 N LEU A 508 17555 17933 15496 3776 -1072 -2294 N
+ATOM 3709 CA LEU A 508 70.654 85.888 -2.287 1.00125.06 C
+ANISOU 3709 CA LEU A 508 16259 16704 14555 3385 -1304 -2382 C
+ATOM 3710 C LEU A 508 72.070 85.983 -1.730 1.00133.75 C
+ANISOU 3710 C LEU A 508 17660 17739 15419 3609 -1705 -2655 C
+ATOM 3711 O LEU A 508 72.775 84.975 -1.650 1.00132.42 O
+ANISOU 3711 O LEU A 508 17581 17530 15202 3562 -1700 -2615 O
+ATOM 3712 CB LEU A 508 70.606 86.404 -3.726 1.00112.64 C
+ANISOU 3712 CB LEU A 508 14312 15095 13392 2907 -1513 -2482 C
+ATOM 3713 CG LEU A 508 69.271 86.186 -4.436 1.00113.17 C
+ANISOU 3713 CG LEU A 508 14056 15174 13769 2653 -1215 -2260 C
+ATOM 3714 CD1 LEU A 508 69.459 86.184 -5.945 1.00106.22 C
+ANISOU 3714 CD1 LEU A 508 12898 14225 13237 2216 -1432 -2343 C
+ATOM 3715 CD2 LEU A 508 68.613 84.894 -3.968 1.00117.32 C
+ANISOU 3715 CD2 LEU A 508 14560 15678 14341 2703 -779 -1932 C
+ATOM 3716 N SER A 509 72.491 87.188 -1.355 1.00130.72 N
+ANISOU 3716 N SER A 509 17414 17317 14936 3856 -2085 -2944 N
+ATOM 3717 CA SER A 509 73.767 87.347 -0.663 1.00136.66 C
+ANISOU 3717 CA SER A 509 18457 17948 15519 4156 -2531 -3236 C
+ATOM 3718 C SER A 509 73.698 86.583 0.646 1.00143.40 C
+ANISOU 3718 C SER A 509 19773 18845 15866 4687 -2319 -3138 C
+ATOM 3719 O SER A 509 74.680 85.977 1.082 1.00138.35 O
+ANISOU 3719 O SER A 509 19358 18121 15090 4839 -2521 -3256 O
+ATOM 3720 CB SER A 509 74.089 88.820 -0.410 1.00130.15 C
+ANISOU 3720 CB SER A 509 17685 17028 14738 4382 -3008 -3572 C
+ATOM 3721 OG SER A 509 74.991 89.319 -1.384 1.00125.27 O
+ANISOU 3721 OG SER A 509 16739 16248 14609 4003 -3376 -3749 O
+ATOM 3722 N SER A 510 72.520 86.615 1.263 1.00144.65 N
+ANISOU 3722 N SER A 510 20078 19123 15761 4999 -1878 -2899 N
+ATOM 3723 CA SER A 510 72.236 85.777 2.417 1.00148.97 C
+ANISOU 3723 CA SER A 510 21044 19713 15846 5526 -1487 -2677 C
+ATOM 3724 C SER A 510 72.424 84.315 2.046 1.00145.48 C
+ANISOU 3724 C SER A 510 20455 19266 15554 5204 -1182 -2426 C
+ATOM 3725 O SER A 510 73.001 83.552 2.811 1.00140.49 O
+ANISOU 3725 O SER A 510 20177 18606 14598 5539 -1145 -2415 O
+ATOM 3726 CB SER A 510 70.807 85.999 2.911 1.00149.05 C
+ANISOU 3726 CB SER A 510 21111 19824 15699 5832 -930 -2348 C
+ATOM 3727 OG SER A 510 70.346 84.882 3.643 1.00147.27 O
+ANISOU 3727 OG SER A 510 21097 19617 15240 6154 -337 -1962 O
+ATOM 3728 N SER A 511 71.946 83.946 0.858 1.00139.39 N
+ANISOU 3728 N SER A 511 19184 18508 15269 4583 -1004 -2249 N
+ATOM 3729 CA SER A 511 72.011 82.573 0.365 1.00129.68 C
+ANISOU 3729 CA SER A 511 17763 17254 14255 4236 -745 -2013 C
+ATOM 3730 C SER A 511 73.437 82.171 0.006 1.00129.30 C
+ANISOU 3730 C SER A 511 17762 17135 14232 4035 -1175 -2258 C
+ATOM 3731 O SER A 511 73.792 80.991 0.047 1.00109.17 O
+ANISOU 3731 O SER A 511 15254 14565 11659 3957 -1019 -2119 O
+ATOM 3732 CB SER A 511 71.108 82.416 -0.862 1.00125.40 C
+ANISOU 3732 CB SER A 511 16701 16703 14243 3684 -564 -1828 C
+ATOM 3733 OG SER A 511 71.167 81.106 -1.394 1.00137.08 O
+ANISOU 3733 OG SER A 511 17990 18125 15969 3359 -392 -1635 O
+ATOM 3734 N GLN A 512 74.247 83.164 -0.347 1.00131.12 N
+ANISOU 3734 N GLN A 512 17958 17304 14560 3957 -1699 -2603 N
+ATOM 3735 CA GLN A 512 75.621 82.941 -0.774 1.00120.52 C
+ANISOU 3735 CA GLN A 512 16587 15845 13361 3755 -2110 -2821 C
+ATOM 3736 C GLN A 512 76.508 82.796 0.431 1.00123.24 C
+ANISOU 3736 C GLN A 512 17385 16120 13322 4264 -2359 -3023 C
+ATOM 3737 O GLN A 512 77.569 82.174 0.385 1.00128.94 O
+ANISOU 3737 O GLN A 512 18162 16749 14081 4188 -2573 -3124 O
+ATOM 3738 CB GLN A 512 76.096 84.150 -1.546 1.00118.44 C
+ANISOU 3738 CB GLN A 512 16077 15483 13440 3537 -2531 -3073 C
+ATOM 3739 CG GLN A 512 76.798 83.822 -2.807 1.00125.91 C
+ANISOU 3739 CG GLN A 512 16711 16343 14787 3048 -2644 -3057 C
+ATOM 3740 CD GLN A 512 76.915 85.020 -3.690 1.00137.22 C
+ANISOU 3740 CD GLN A 512 17859 17690 16589 2843 -2877 -3186 C
+ATOM 3741 OE1 GLN A 512 77.456 86.052 -3.281 1.00153.03 O
+ANISOU 3741 OE1 GLN A 512 19904 19568 18672 3053 -3245 -3442 O
+ATOM 3742 NE2 GLN A 512 76.353 84.922 -4.897 1.00128.62 N
+ANISOU 3742 NE2 GLN A 512 16487 16643 15739 2470 -2678 -3017 N
+ATOM 3743 N GLY A 513 76.073 83.422 1.510 1.00128.93 N
+ANISOU 3743 N GLY A 513 18453 16869 13665 4826 -2362 -3100 N
+ATOM 3744 CA GLY A 513 76.767 83.309 2.761 1.00135.31 C
+ANISOU 3744 CA GLY A 513 19790 17602 14021 5449 -2610 -3308 C
+ATOM 3745 C GLY A 513 76.597 81.908 3.295 1.00133.10 C
+ANISOU 3745 C GLY A 513 19748 17398 13425 5620 -2132 -3010 C
+ATOM 3746 O GLY A 513 77.464 81.407 3.988 1.00135.48 O
+ANISOU 3746 O GLY A 513 20407 17622 13448 5952 -2344 -3163 O
+ATOM 3747 N THR A 514 75.478 81.270 2.971 1.00130.00 N
+ANISOU 3747 N THR A 514 19139 17128 13128 5402 -1499 -2584 N
+ATOM 3748 CA THR A 514 75.252 79.899 3.409 1.00136.05 C
+ANISOU 3748 CA THR A 514 20053 17932 13707 5525 -990 -2248 C
+ATOM 3749 C THR A 514 76.125 78.980 2.571 1.00136.91 C
+ANISOU 3749 C THR A 514 19914 17993 14111 4991 -1151 -2279 C
+ATOM 3750 O THR A 514 76.451 77.859 2.971 1.00136.85 O
+ANISOU 3750 O THR A 514 20093 17981 13923 5102 -944 -2139 O
+ATOM 3751 CB THR A 514 73.784 79.475 3.234 1.00141.83 C
+ANISOU 3751 CB THR A 514 20522 18734 14631 5408 -287 -1768 C
+ATOM 3752 OG1 THR A 514 73.591 78.921 1.927 1.00142.93 O
+ANISOU 3752 OG1 THR A 514 20113 18858 15336 4676 -233 -1640 O
+ATOM 3753 CG2 THR A 514 72.861 80.659 3.413 1.00145.09 C
+ANISOU 3753 CG2 THR A 514 20916 19192 15018 5620 -214 -1761 C
+ATOM 3754 N ILE A 515 76.491 79.473 1.394 1.00129.08 N
+ANISOU 3754 N ILE A 515 18518 16960 13565 4442 -1494 -2442 N
+ATOM 3755 CA ILE A 515 77.327 78.735 0.468 1.00119.39 C
+ANISOU 3755 CA ILE A 515 17053 15677 12633 3951 -1657 -2465 C
+ATOM 3756 C ILE A 515 78.787 78.796 0.895 1.00127.05 C
+ANISOU 3756 C ILE A 515 18275 16524 13475 4143 -2161 -2798 C
+ATOM 3757 O ILE A 515 79.482 77.778 0.906 1.00128.44 O
+ANISOU 3757 O ILE A 515 18530 16671 13600 4065 -2153 -2760 O
+ATOM 3758 CB ILE A 515 77.220 79.308 -0.945 1.00110.42 C
+ANISOU 3758 CB ILE A 515 15452 14516 11987 3401 -1815 -2500 C
+ATOM 3759 CG1 ILE A 515 75.801 79.150 -1.481 1.00109.39 C
+ANISOU 3759 CG1 ILE A 515 15038 14466 12060 3177 -1388 -2203 C
+ATOM 3760 CG2 ILE A 515 78.168 78.587 -1.861 1.00112.80 C
+ANISOU 3760 CG2 ILE A 515 15581 14743 12533 2997 -1979 -2516 C
+ATOM 3761 CD1 ILE A 515 75.570 79.879 -2.780 1.00110.01 C
+ANISOU 3761 CD1 ILE A 515 14740 14519 12538 2759 -1561 -2268 C
+ATOM 3762 N GLU A 516 79.240 79.996 1.247 1.00122.76 N
+ANISOU 3762 N GLU A 516 17837 15878 12927 4400 -2627 -3132 N
+ATOM 3763 CA GLU A 516 80.636 80.218 1.589 1.00124.18 C
+ANISOU 3763 CA GLU A 516 18172 15860 13149 4571 -3208 -3493 C
+ATOM 3764 C GLU A 516 81.099 79.274 2.681 1.00126.09 C
+ANISOU 3764 C GLU A 516 18894 16095 12918 5029 -3183 -3522 C
+ATOM 3765 O GLU A 516 82.117 78.595 2.539 1.00116.84 O
+ANISOU 3765 O GLU A 516 17721 14825 11848 4893 -3381 -3605 O
+ATOM 3766 CB GLU A 516 80.863 81.656 2.046 1.00135.21 C
+ANISOU 3766 CB GLU A 516 19658 17112 14603 4907 -3722 -3854 C
+ATOM 3767 CG GLU A 516 82.315 82.045 1.962 1.00146.41 C
+ANISOU 3767 CG GLU A 516 20992 18238 16400 4885 -4381 -4215 C
+ATOM 3768 CD GLU A 516 82.865 81.775 0.582 1.00151.28 C
+ANISOU 3768 CD GLU A 516 21100 18789 17590 4220 -4329 -4073 C
+ATOM 3769 OE1 GLU A 516 82.373 82.413 -0.367 1.00146.52 O
+ANISOU 3769 OE1 GLU A 516 20133 18221 17316 3867 -4198 -3957 O
+ATOM 3770 OE2 GLU A 516 83.763 80.917 0.441 1.00154.24 O
+ANISOU 3770 OE2 GLU A 516 21471 19078 18055 4089 -4397 -4065 O
+END
--- /dev/null
+TITLE STRUCTURE OF TANK-BINDING KINASE 1 (Truncated test file)
+ATOM 3510 N LEU A 468 76.337 90.332 -7.628 1.00168.53 N
+ANISOU 3510 N LEU A 468 19760 15191 29082 5189 1248 -1702 N
+ATOM 3511 CA LEU A 468 75.576 90.788 -6.476 1.00181.60 C
+ANISOU 3511 CA LEU A 468 21073 16927 30998 5158 1421 -2051 C
+ATOM 3512 C LEU A 468 76.285 91.971 -5.836 1.00196.57 C
+ANISOU 3512 C LEU A 468 23029 18636 33021 5053 1667 -2229 C
+ATOM 3513 O LEU A 468 75.727 93.067 -5.733 1.00197.97 O
+ANISOU 3513 O LEU A 468 23115 18581 33523 5166 1662 -2304 O
+ATOM 3514 CB LEU A 468 75.409 89.671 -5.449 1.00173.72 C
+ANISOU 3514 CB LEU A 468 19829 16340 29836 4981 1593 -2304 C
+ATOM 3515 CG LEU A 468 74.099 88.882 -5.420 1.00170.58 C
+ANISOU 3515 CG LEU A 468 19142 16142 29529 5074 1449 -2345 C
+ATOM 3516 CD1 LEU A 468 74.023 87.940 -6.581 1.00167.98 C
+ANISOU 3516 CD1 LEU A 468 18951 15858 29015 5180 1156 -2025 C
+ATOM 3517 CD2 LEU A 468 73.988 88.096 -4.145 1.00165.16 C
+ANISOU 3517 CD2 LEU A 468 18217 15818 28720 4865 1706 -2656 C
+ATOM 3518 N ASP A 469 77.529 91.753 -5.429 1.00208.80 N
+ANISOU 3518 N ASP A 469 24731 20282 34322 4836 1875 -2296 N
+ATOM 3519 CA ASP A 469 78.267 92.785 -4.720 1.00223.11 C
+ANISOU 3519 CA ASP A 469 26577 21960 36233 4701 2123 -2500 C
+ATOM 3520 C ASP A 469 78.653 93.973 -5.599 1.00231.96 C
+ANISOU 3520 C ASP A 469 27954 22654 37525 4817 2037 -2283 C
+ATOM 3521 O ASP A 469 78.718 95.100 -5.118 1.00235.71 O
+ANISOU 3521 O ASP A 469 28377 22940 38242 4798 2175 -2449 O
+ATOM 3522 CB ASP A 469 79.506 92.197 -4.057 1.00224.50 C
+ANISOU 3522 CB ASP A 469 26841 22370 36089 4433 2350 -2633 C
+ATOM 3523 CG ASP A 469 79.748 92.767 -2.679 1.00229.51 C
+ANISOU 3523 CG ASP A 469 27303 23107 36794 4254 2637 -3018 C
+ATOM 3524 OD1 ASP A 469 79.958 93.992 -2.564 1.00232.36 O
+ANISOU 3524 OD1 ASP A 469 27695 23203 37387 4262 2718 -3093 O
+ATOM 3525 OD2 ASP A 469 79.751 91.979 -1.709 1.00229.48 O
+ANISOU 3525 OD2 ASP A 469 27145 23450 36598 4098 2779 -3242 O
+ATOM 3526 N PHE A 470 78.904 93.735 -6.882 1.00233.88 N
+ANISOU 3526 N PHE A 470 28481 22742 37641 4931 1813 -1912 N
+ATOM 3527 CA PHE A 470 79.292 94.831 -7.766 1.00237.73 C
+ANISOU 3527 CA PHE A 470 29252 22819 38256 5033 1733 -1677 C
+ATOM 3528 C PHE A 470 78.103 95.470 -8.467 1.00232.15 C
+ANISOU 3528 C PHE A 470 28512 21868 37828 5322 1470 -1512 C
+ATOM 3529 O PHE A 470 78.021 96.691 -8.532 1.00230.69 O
+ANISOU 3529 O PHE A 470 28371 21372 37909 5402 1493 -1517 O
+ATOM 3530 CB PHE A 470 80.344 94.379 -8.784 1.00242.99 C
+ANISOU 3530 CB PHE A 470 30297 23410 38616 4976 1661 -1357 C
+ATOM 3531 CG PHE A 470 80.663 95.388 -9.839 1.00251.53 C
+ANISOU 3531 CG PHE A 470 31709 24074 39788 5089 1550 -1064 C
+ATOM 3532 CD1 PHE A 470 81.658 96.315 -9.620 1.00252.90 C
+ANISOU 3532 CD1 PHE A 470 32021 24036 40032 4942 1771 -1133 C
+ATOM 3533 CD2 PHE A 470 80.005 95.389 -11.059 1.00255.02 C
+ANISOU 3533 CD2 PHE A 470 32335 24339 40221 5330 1225 -715 C
+ATOM 3534 CE1 PHE A 470 81.981 97.242 -10.575 1.00254.75 C
+ANISOU 3534 CE1 PHE A 470 32569 23879 40344 5028 1688 -862 C
+ATOM 3535 CE2 PHE A 470 80.321 96.320 -12.027 1.00256.76 C
+ANISOU 3535 CE2 PHE A 470 32894 24173 40491 5427 1126 -433 C
+ATOM 3536 CZ PHE A 470 81.313 97.248 -11.784 1.00256.57 C
+ANISOU 3536 CZ PHE A 470 33006 23929 40550 5272 1365 -504 C
+ATOM 3537 N CYS A 471 77.190 94.665 -8.997 1.00176.88 N
+ANISOU 3537 N CYS A 471 20955 21812 24441 2225 -3821 -3711 N
+ATOM 3538 CA CYS A 471 76.124 95.233 -9.815 1.00176.41 C
+ANISOU 3538 CA CYS A 471 20820 21906 24301 2124 -3576 -3614 C
+ATOM 3539 C CYS A 471 74.868 95.631 -9.050 1.00176.82 C
+ANISOU 3539 C CYS A 471 21026 22206 23952 2247 -3588 -3734 C
+ATOM 3540 O CYS A 471 74.632 96.811 -8.854 1.00178.66 O
+ANISOU 3540 O CYS A 471 21175 22393 24314 2353 -3749 -3873 O
+ATOM 3541 CB CYS A 471 75.805 94.346 -11.019 1.00173.95 C
+ANISOU 3541 CB CYS A 471 20521 21694 23877 1925 -3217 -3359 C
+ATOM 3542 SG CYS A 471 76.954 94.571 -12.398 1.00273.04 S
+ANISOU 3542 SG CYS A 471 32850 33934 36957 1863 -3075 -3146 S
+ATOM 3543 N ILE A 472 74.068 94.670 -8.603 1.00173.50 N
+ANISOU 3543 N ILE A 472 20813 22023 23085 2253 -3402 -3662 N
+ATOM 3544 CA ILE A 472 72.771 95.033 -8.022 1.00171.09 C
+ANISOU 3544 CA ILE A 472 20616 21936 22453 2374 -3307 -3694 C
+ATOM 3545 C ILE A 472 72.832 96.022 -6.874 1.00177.82 C
+ANISOU 3545 C ILE A 472 21591 22750 23222 2698 -3611 -3931 C
+ATOM 3546 O ILE A 472 71.992 96.914 -6.776 1.00182.92 O
+ANISOU 3546 O ILE A 472 22220 23491 23792 2778 -3598 -3985 O
+ATOM 3547 CB ILE A 472 71.979 93.843 -7.518 1.00159.41 C
+ANISOU 3547 CB ILE A 472 19318 20653 20599 2393 -3038 -3546 C
+ATOM 3548 CG1 ILE A 472 70.708 93.667 -8.341 1.00147.27 C
+ANISOU 3548 CG1 ILE A 472 17653 19253 19051 2196 -2745 -3384 C
+ATOM 3549 CG2 ILE A 472 71.526 94.090 -6.105 1.00155.95 C
+ANISOU 3549 CG2 ILE A 472 19129 20312 19812 2752 -3085 -3637 C
+ATOM 3550 CD1 ILE A 472 70.927 92.915 -9.606 1.00135.92 C
+ANISOU 3550 CD1 ILE A 472 16097 17752 17794 1929 -2643 -3254 C
+ATOM 3551 N ARG A 473 73.812 95.865 -5.996 1.00180.33 N
+ANISOU 3551 N ARG A 473 22055 22917 23544 2920 -3920 -4092 N
+ATOM 3552 CA ARG A 473 73.860 96.762 -4.877 1.00189.65 C
+ANISOU 3552 CA ARG A 473 23415 24034 24610 3307 -4283 -4357 C
+ATOM 3553 C ARG A 473 74.328 98.021 -5.558 1.00185.98 C
+ANISOU 3553 C ARG A 473 22628 23344 24692 3195 -4530 -4477 C
+ATOM 3554 O ARG A 473 73.519 98.885 -5.866 1.00181.76 O
+ANISOU 3554 O ARG A 473 22002 22904 24153 3165 -4446 -4474 O
+ATOM 3555 CB ARG A 473 74.803 96.287 -3.768 1.00205.24 C
+ANISOU 3555 CB ARG A 473 25661 25862 26460 3635 -4629 -4545 C
+ATOM 3556 CG ARG A 473 74.468 96.921 -2.433 1.00220.50 C
+ANISOU 3556 CG ARG A 473 27955 27814 28011 4171 -4923 -4787 C
+ATOM 3557 CD ARG A 473 75.337 96.433 -1.295 1.00232.58 C
+ANISOU 3557 CD ARG A 473 29837 29192 29341 4591 -5300 -5003 C
+ATOM 3558 NE ARG A 473 76.763 96.602 -1.549 1.00237.46 N
+ANISOU 3558 NE ARG A 473 30220 29440 30564 4489 -5773 -5205 N
+ATOM 3559 CZ ARG A 473 77.716 95.991 -0.861 1.00240.32 C
+ANISOU 3559 CZ ARG A 473 30786 29623 30903 4725 -6098 -5371 C
+ATOM 3560 NH1 ARG A 473 77.388 95.172 0.115 1.00241.12 N
+ANISOU 3560 NH1 ARG A 473 31370 29900 30344 5100 -5978 -5355 N
+ATOM 3561 NH2 ARG A 473 78.988 96.195 -1.159 1.00241.54 N
+ANISOU 3561 NH2 ARG A 473 30651 29398 31724 4605 -6518 -5533 N
+ATOM 3562 N ASN A 474 75.608 98.073 -5.901 1.00188.74 N
+ANISOU 3562 N ASN A 474 22768 23381 25563 3107 -4772 -4534 N
+ATOM 3563 CA ASN A 474 76.168 99.264 -6.526 1.00188.61 C
+ANISOU 3563 CA ASN A 474 22395 23075 26194 3026 -4977 -4605 C
+ATOM 3564 C ASN A 474 75.420 99.892 -7.729 1.00173.98 C
+ANISOU 3564 C ASN A 474 20312 21326 24467 2781 -4623 -4414 C
+ATOM 3565 O ASN A 474 75.482 101.107 -7.891 1.00176.08 O
+ANISOU 3565 O ASN A 474 20374 21426 25104 2827 -4803 -4518 O
+ATOM 3566 CB ASN A 474 77.650 99.066 -6.857 1.00199.45 C
+ANISOU 3566 CB ASN A 474 23514 24060 28207 2939 -5170 -4595 C
+ATOM 3567 CG ASN A 474 78.504 98.809 -5.625 1.00210.23 C
+ANISOU 3567 CG ASN A 474 25062 25219 29597 3243 -5689 -4883 C
+ATOM 3568 OD1 ASN A 474 78.174 99.240 -4.527 1.00215.26 O
+ANISOU 3568 OD1 ASN A 474 25969 25891 29928 3596 -6043 -5160 O
+ATOM 3569 ND2 ASN A 474 79.613 98.103 -5.810 1.00212.07 N
+ANISOU 3569 ND2 ASN A 474 25176 25222 30179 3148 -5748 -4822 N
+ATOM 3570 N ILE A 475 74.722 99.114 -8.562 1.00161.86 N
+ANISOU 3570 N ILE A 475 18813 20033 22652 2556 -4165 -4158 N
+ATOM 3571 CA ILE A 475 74.022 99.727 -9.709 1.00154.84 C
+ANISOU 3571 CA ILE A 475 17755 19216 21861 2390 -3885 -4015 C
+ATOM 3572 C ILE A 475 72.785 100.520 -9.312 1.00159.27 C
+ANISOU 3572 C ILE A 475 18401 19995 22121 2490 -3891 -4125 C
+ATOM 3573 O ILE A 475 72.662 101.687 -9.663 1.00162.60 O
+ANISOU 3573 O ILE A 475 18651 20327 22804 2505 -3962 -4186 O
+ATOM 3574 CB ILE A 475 73.600 98.727 -10.818 1.00214.93 C
+ANISOU 3574 CB ILE A 475 25397 26975 29293 2173 -3475 -3753 C
+ATOM 3575 CG1 ILE A 475 74.808 98.227 -11.613 1.00218.74 C
+ANISOU 3575 CG1 ILE A 475 25753 27211 30145 2083 -3390 -3585 C
+ATOM 3576 CG2 ILE A 475 72.618 99.379 -11.789 1.00210.37 C
+ANISOU 3576 CG2 ILE A 475 24743 26509 28681 2097 -3256 -3677 C
+ATOM 3577 CD1 ILE A 475 74.446 97.201 -12.664 1.00218.15 C
+ANISOU 3577 CD1 ILE A 475 25777 27260 29850 1946 -3056 -3359 C
+ATOM 3578 N GLU A 476 71.856 99.893 -8.600 1.00156.45 N
+ANISOU 3578 N GLU A 476 18293 19907 21245 2571 -3778 -4120 N
+ATOM 3579 CA GLU A 476 70.623 100.594 -8.252 1.00142.72 C
+ANISOU 3579 CA GLU A 476 16627 18370 19231 2677 -3720 -4176 C
+ATOM 3580 C GLU A 476 70.845 101.560 -7.094 1.00144.41 C
+ANISOU 3580 C GLU A 476 16959 18500 19412 3012 -4114 -4440 C
+ATOM 3581 O GLU A 476 70.012 102.417 -6.811 1.00142.58 O
+ANISOU 3581 O GLU A 476 16768 18380 19024 3141 -4136 -4517 O
+ATOM 3582 CB GLU A 476 69.486 99.616 -7.958 1.00128.68 C
+ANISOU 3582 CB GLU A 476 15020 16860 17012 2665 -3395 -4018 C
+ATOM 3583 CG GLU A 476 69.562 98.905 -6.628 1.00128.73 C
+ANISOU 3583 CG GLU A 476 15321 16930 16662 2941 -3433 -4041 C
+ATOM 3584 CD GLU A 476 68.465 97.866 -6.484 1.00133.35 C
+ANISOU 3584 CD GLU A 476 15992 17719 16955 2900 -3026 -3806 C
+ATOM 3585 OE1 GLU A 476 68.285 97.061 -7.422 1.00132.30 O
+ANISOU 3585 OE1 GLU A 476 15710 17598 16962 2603 -2816 -3643 O
+ATOM 3586 OE2 GLU A 476 67.768 97.860 -5.448 1.00136.37 O
+ANISOU 3586 OE2 GLU A 476 16588 18223 17003 3196 -2912 -3773 O
+ATOM 3587 N LYS A 477 71.990 101.424 -6.439 1.00148.46 N
+ANISOU 3587 N LYS A 477 17534 18788 20087 3179 -4467 -4596 N
+ATOM 3588 CA LYS A 477 72.399 102.365 -5.405 1.00154.25 C
+ANISOU 3588 CA LYS A 477 18378 19348 20882 3544 -4976 -4907 C
+ATOM 3589 C LYS A 477 72.634 103.732 -5.994 1.00159.76 C
+ANISOU 3589 C LYS A 477 18754 19833 22117 3467 -5183 -5014 C
+ATOM 3590 O LYS A 477 72.568 104.742 -5.292 1.00158.01 O
+ANISOU 3590 O LYS A 477 18598 19516 21921 3749 -5568 -5266 O
+ATOM 3591 CB LYS A 477 73.667 101.883 -4.706 1.00154.03 C
+ANISOU 3591 CB LYS A 477 18446 19057 21022 3730 -5372 -5076 C
+ATOM 3592 CG LYS A 477 73.367 100.787 -3.750 1.00149.76 C
+ANISOU 3592 CG LYS A 477 18324 18717 19861 3975 -5258 -5042 C
+ATOM 3593 CD LYS A 477 74.437 100.554 -2.740 1.00143.39 C
+ANISOU 3593 CD LYS A 477 17737 17664 19082 4327 -5762 -5306 C
+ATOM 3594 CE LYS A 477 73.739 100.087 -1.488 1.00145.72 C
+ANISOU 3594 CE LYS A 477 18569 18186 18613 4805 -5697 -5337 C
+ATOM 3595 NZ LYS A 477 74.661 99.556 -0.469 1.00149.42 N
+ANISOU 3595 NZ LYS A 477 19366 18470 18936 5206 -6108 -5561 N
+ATOM 3596 N THR A 478 72.908 103.757 -7.293 1.00166.45 N
+ANISOU 3596 N THR A 478 19271 20589 23384 3124 -4918 -4810 N
+ATOM 3597 CA THR A 478 73.186 105.012 -7.968 1.00170.99 C
+ANISOU 3597 CA THR A 478 19509 20929 24531 3052 -5023 -4844 C
+ATOM 3598 C THR A 478 71.905 105.733 -8.391 1.00172.33 C
+ANISOU 3598 C THR A 478 19686 21358 24435 2999 -4780 -4796 C
+ATOM 3599 O THR A 478 71.021 105.170 -9.046 1.00163.10 O
+ANISOU 3599 O THR A 478 18581 20461 22928 2823 -4356 -4594 O
+ATOM 3600 CB THR A 478 74.217 104.856 -9.128 1.00146.93 C
+ANISOU 3600 CB THR A 478 16115 17589 22125 2815 -4843 -4626 C
+ATOM 3601 OG1 THR A 478 74.873 106.106 -9.369 1.00147.15 O
+ANISOU 3601 OG1 THR A 478 15790 17239 22881 2857 -5085 -4705 O
+ATOM 3602 CG2 THR A 478 73.562 104.391 -10.425 1.00144.32 C
+ANISOU 3602 CG2 THR A 478 15764 17473 21597 2570 -4282 -4318 C
+ATOM 3603 N VAL A 479 71.809 106.979 -7.944 1.00177.73 N
+ANISOU 3603 N VAL A 479 20309 21929 25291 3181 -5110 -5014 N
+ATOM 3604 CA VAL A 479 70.674 107.838 -8.218 1.00175.65 C
+ANISOU 3604 CA VAL A 479 20044 21875 24819 3171 -4959 -5013 C
+ATOM 3605 C VAL A 479 71.176 109.077 -8.939 1.00177.67 C
+ANISOU 3605 C VAL A 479 19928 21830 25749 3101 -5069 -5035 C
+ATOM 3606 O VAL A 479 72.353 109.417 -8.840 1.00179.02 O
+ANISOU 3606 O VAL A 479 19865 21600 26555 3150 -5387 -5121 O
+ATOM 3607 CB VAL A 479 69.983 108.266 -6.909 1.00168.37 C
+ANISOU 3607 CB VAL A 479 19442 21113 23418 3524 -5243 -5249 C
+ATOM 3608 CG1 VAL A 479 69.008 109.403 -7.169 1.00162.23 C
+ANISOU 3608 CG1 VAL A 479 18603 20470 22565 3531 -5176 -5285 C
+ATOM 3609 CG2 VAL A 479 69.288 107.080 -6.256 1.00163.89 C
+ANISOU 3609 CG2 VAL A 479 19236 20856 22180 3624 -4991 -5142 C
+ATOM 3610 N MET A 486 57.931 103.433 -6.150 1.00 92.00 N
+ANISOU 3610 N MET A 486 10154 13425 11375 3371 -1523 -3283 N
+ATOM 3611 CA MET A 486 56.824 104.104 -5.482 1.00110.61 C
+ANISOU 3611 CA MET A 486 12558 15882 13585 3644 -1287 -3161 C
+ATOM 3612 C MET A 486 56.182 105.150 -6.389 1.00111.38 C
+ANISOU 3612 C MET A 486 12428 16016 13877 3424 -1416 -3308 C
+ATOM 3613 O MET A 486 56.000 106.305 -6.002 1.00120.35 O
+ANISOU 3613 O MET A 486 13691 17243 14794 3639 -1526 -3430 O
+ATOM 3614 CB MET A 486 57.288 104.743 -4.170 1.00120.60 C
+ANISOU 3614 CB MET A 486 14253 17221 14347 4174 -1395 -3243 C
+ATOM 3615 CG MET A 486 58.405 105.768 -4.316 1.00126.87 C
+ANISOU 3615 CG MET A 486 15171 17987 15047 4196 -1944 -3629 C
+ATOM 3616 SD MET A 486 58.150 107.169 -3.210 1.00146.78 S
+ANISOU 3616 SD MET A 486 18044 20597 17128 4757 -2124 -3782 S
+ATOM 3617 CE MET A 486 58.003 106.326 -1.640 1.00102.35 C
+ANISOU 3617 CE MET A 486 12883 15002 11003 5391 -1797 -3524 C
+ATOM 3618 N GLY A 496 57.154 99.412 -2.065 1.00157.62 N
+ANISOU 3618 N GLY A 496 19150 21656 19083 4616 82 -2024 N
+ATOM 3619 CA GLY A 496 57.031 99.217 -3.498 1.00158.07 C
+ANISOU 3619 CA GLY A 496 18749 21636 19677 3991 -116 -2141 C
+ATOM 3620 C GLY A 496 57.664 97.914 -3.942 1.00163.71 C
+ANISOU 3620 C GLY A 496 19349 22235 20619 3709 -140 -2093 C
+ATOM 3621 O GLY A 496 58.040 97.090 -3.111 1.00167.17 O
+ANISOU 3621 O GLY A 496 20009 22652 20858 3970 79 -1915 O
+ATOM 3622 N GLU A 497 57.778 97.722 -5.254 1.00166.67 N
+ANISOU 3622 N GLU A 497 19413 22530 21383 3222 -403 -2250 N
+ATOM 3623 CA GLU A 497 58.431 96.534 -5.792 1.00170.73 C
+ANISOU 3623 CA GLU A 497 19840 22933 22098 2955 -485 -2239 C
+ATOM 3624 C GLU A 497 59.931 96.621 -5.556 1.00172.64 C
+ANISOU 3624 C GLU A 497 20403 23228 21965 3043 -809 -2472 C
+ATOM 3625 O GLU A 497 60.589 95.609 -5.311 1.00173.01 O
+ANISOU 3625 O GLU A 497 20547 23223 21965 3047 -764 -2395 O
+ATOM 3626 CB GLU A 497 58.173 96.394 -7.290 1.00169.62 C
+ANISOU 3626 CB GLU A 497 19361 22681 22408 2505 -727 -2374 C
+ATOM 3627 CG GLU A 497 56.882 97.012 -7.777 1.00173.11 C
+ANISOU 3627 CG GLU A 497 19518 23086 23171 2413 -663 -2350 C
+ATOM 3628 CD GLU A 497 56.703 96.840 -9.270 1.00173.61 C
+ANISOU 3628 CD GLU A 497 19329 23013 23621 2054 -974 -2531 C
+ATOM 3629 OE1 GLU A 497 57.597 96.241 -9.908 1.00170.78 O
+ANISOU 3629 OE1 GLU A 497 19040 22600 23250 1901 -1202 -2647 O
+ATOM 3630 OE2 GLU A 497 55.672 97.300 -9.805 1.00174.73 O
+ANISOU 3630 OE2 GLU A 497 19233 23093 24064 1967 -999 -2559 O
+ATOM 3631 N ILE A 498 60.466 97.836 -5.652 1.00171.44 N
+ANISOU 3631 N ILE A 498 20381 23149 21608 3107 -1147 -2757 N
+ATOM 3632 CA ILE A 498 61.883 98.078 -5.403 1.00167.93 C
+ANISOU 3632 CA ILE A 498 20186 22695 20926 3210 -1503 -2995 C
+ATOM 3633 C ILE A 498 62.251 97.620 -4.004 1.00173.82 C
+ANISOU 3633 C ILE A 498 21298 23465 21280 3659 -1379 -2903 C
+ATOM 3634 O ILE A 498 63.315 97.034 -3.789 1.00168.12 O
+ANISOU 3634 O ILE A 498 20732 22684 20462 3692 -1544 -2980 O
+ATOM 3635 CB ILE A 498 62.227 99.564 -5.520 1.00165.53 C
+ANISOU 3635 CB ILE A 498 19934 22420 20540 3287 -1855 -3283 C
+ATOM 3636 CG1 ILE A 498 61.848 100.100 -6.901 1.00171.37 C
+ANISOU 3636 CG1 ILE A 498 20360 23137 21618 2911 -1947 -3365 C
+ATOM 3637 CG2 ILE A 498 63.706 99.798 -5.239 1.00153.61 C
+ANISOU 3637 CG2 ILE A 498 18613 20820 18931 3398 -2256 -3525 C
+ATOM 3638 CD1 ILE A 498 61.891 101.605 -6.996 1.00174.73 C
+ANISOU 3638 CD1 ILE A 498 20793 23594 22004 2996 -2195 -3587 C
+ATOM 3639 N SER A 499 61.362 97.890 -3.054 1.00187.32 N
+ANISOU 3639 N SER A 499 23169 25252 22753 4049 -1074 -2727 N
+ATOM 3640 CA SER A 499 61.558 97.444 -1.683 1.00198.47 C
+ANISOU 3640 CA SER A 499 24999 26682 23729 4594 -880 -2593 C
+ATOM 3641 C SER A 499 61.611 95.926 -1.651 1.00206.95 C
+ANISOU 3641 C SER A 499 26003 27687 24943 4481 -548 -2315 C
+ATOM 3642 O SER A 499 62.302 95.334 -0.823 1.00211.11 O
+ANISOU 3642 O SER A 499 26867 28195 25151 4806 -533 -2293 O
+ATOM 3643 CB SER A 499 60.435 97.952 -0.780 1.00200.16 C
+ANISOU 3643 CB SER A 499 25385 26976 23690 5064 -498 -2368 C
+ATOM 3644 OG SER A 499 60.635 97.541 0.556 1.00203.12 O
+ANISOU 3644 OG SER A 499 26244 27359 23574 5697 -286 -2224 O
+ATOM 3645 N ASP A 500 60.877 95.300 -2.564 1.00209.43 N
+ANISOU 3645 N ASP A 500 25883 27938 25751 4040 -320 -2123 N
+ATOM 3646 CA ASP A 500 60.862 93.851 -2.655 1.00212.36 C
+ANISOU 3646 CA ASP A 500 26120 28207 26361 3883 -39 -1865 C
+ATOM 3647 C ASP A 500 62.097 93.307 -3.366 1.00203.21 C
+ANISOU 3647 C ASP A 500 24946 26999 25265 3557 -426 -2093 C
+ATOM 3648 O ASP A 500 62.511 92.195 -3.092 1.00204.96 O
+ANISOU 3648 O ASP A 500 25238 27165 25472 3573 -286 -1954 O
+ATOM 3649 CB ASP A 500 59.580 93.355 -3.335 1.00221.23 C
+ANISOU 3649 CB ASP A 500 26765 29217 28075 3573 287 -1593 C
+ATOM 3650 CG ASP A 500 58.346 93.583 -2.486 1.00233.55 C
+ANISOU 3650 CG ASP A 500 28310 30773 29657 3938 816 -1243 C
+ATOM 3651 OD1 ASP A 500 58.502 93.807 -1.272 1.00239.09 O
+ANISOU 3651 OD1 ASP A 500 29432 31558 29852 4492 1029 -1137 O
+ATOM 3652 OD2 ASP A 500 57.226 93.532 -3.034 1.00237.24 O
+ANISOU 3652 OD2 ASP A 500 28355 31128 30656 3709 1011 -1072 O
+ATOM 3653 N ILE A 501 62.692 94.094 -4.258 1.00192.67 N
+ANISOU 3653 N ILE A 501 23525 25673 24008 3292 -875 -2413 N
+ATOM 3654 CA ILE A 501 63.864 93.633 -5.007 1.00181.71 C
+ANISOU 3654 CA ILE A 501 22108 24215 22719 3006 -1195 -2587 C
+ATOM 3655 C ILE A 501 65.165 93.699 -4.196 1.00170.68 C
+ANISOU 3655 C ILE A 501 21064 22814 20972 3287 -1450 -2764 C
+ATOM 3656 O ILE A 501 65.940 92.735 -4.173 1.00164.70 O
+ANISOU 3656 O ILE A 501 20376 21999 20202 3222 -1476 -2736 O
+ATOM 3657 CB ILE A 501 64.023 94.385 -6.353 1.00138.03 C
+ANISOU 3657 CB ILE A 501 16341 18649 17453 2657 -1507 -2802 C
+ATOM 3658 CG1 ILE A 501 63.385 93.589 -7.491 1.00130.33 C
+ANISOU 3658 CG1 ILE A 501 15061 17587 16872 2296 -1411 -2683 C
+ATOM 3659 CG2 ILE A 501 65.491 94.642 -6.682 1.00137.98 C
+ANISOU 3659 CG2 ILE A 501 16437 18581 17410 2596 -1883 -3037 C
+ATOM 3660 CD1 ILE A 501 61.877 93.516 -7.426 1.00127.50 C
+ANISOU 3660 CD1 ILE A 501 14480 17217 16748 2292 -1111 -2482 C
+ATOM 3661 N HIS A 502 65.396 94.829 -3.532 1.00164.00 N
+ANISOU 3661 N HIS A 502 20439 22007 19869 3613 -1676 -2964 N
+ATOM 3662 CA HIS A 502 66.603 95.022 -2.737 1.00157.69 C
+ANISOU 3662 CA HIS A 502 19968 21147 18800 3931 -2029 -3195 C
+ATOM 3663 C HIS A 502 66.627 94.018 -1.594 1.00162.64 C
+ANISOU 3663 C HIS A 502 20933 21795 19069 4322 -1761 -3012 C
+ATOM 3664 O HIS A 502 67.677 93.496 -1.229 1.00164.35 O
+ANISOU 3664 O HIS A 502 21348 21935 19163 4433 -1971 -3125 O
+ATOM 3665 CB HIS A 502 66.654 96.452 -2.195 1.00150.83 C
+ANISOU 3665 CB HIS A 502 19272 20282 17755 4264 -2351 -3452 C
+ATOM 3666 CG HIS A 502 67.989 97.117 -2.348 1.00143.78 C
+ANISOU 3666 CG HIS A 502 18387 19223 17019 4248 -2929 -3804 C
+ATOM 3667 ND1 HIS A 502 68.672 97.155 -3.544 1.00137.00 N
+ANISOU 3667 ND1 HIS A 502 17193 18253 16609 3785 -3096 -3872 N
+ATOM 3668 CD2 HIS A 502 68.759 97.787 -1.457 1.00140.15 C
+ANISOU 3668 CD2 HIS A 502 18217 18647 16387 4674 -3387 -4099 C
+ATOM 3669 CE1 HIS A 502 69.807 97.814 -3.383 1.00131.33 C
+ANISOU 3669 CE1 HIS A 502 16503 17343 16055 3893 -3583 -4155 C
+ATOM 3670 NE2 HIS A 502 69.883 98.208 -2.125 1.00130.34 N
+ANISOU 3670 NE2 HIS A 502 16741 17200 15583 4416 -3815 -4326 N
+ATOM 3671 N THR A 503 65.450 93.751 -1.039 1.00163.37 N
+ANISOU 3671 N THR A 503 21080 21971 19022 4552 -1268 -2705 N
+ATOM 3672 CA THR A 503 65.295 92.771 0.033 1.00163.31 C
+ANISOU 3672 CA THR A 503 21384 21972 18696 4974 -872 -2437 C
+ATOM 3673 C THR A 503 65.393 91.327 -0.475 1.00151.49 C
+ANISOU 3673 C THR A 503 19659 20415 17484 4610 -614 -2206 C
+ATOM 3674 O THR A 503 65.955 90.464 0.198 1.00146.11 O
+ANISOU 3674 O THR A 503 19247 19705 16563 4853 -520 -2130 O
+ATOM 3675 CB THR A 503 63.956 92.972 0.783 1.00170.09 C
+ANISOU 3675 CB THR A 503 22342 22899 19387 5379 -334 -2106 C
+ATOM 3676 OG1 THR A 503 64.026 94.162 1.576 1.00176.61 O
+ANISOU 3676 OG1 THR A 503 23551 23775 19778 5902 -585 -2325 O
+ATOM 3677 CG2 THR A 503 63.645 91.790 1.693 1.00171.53 C
+ANISOU 3677 CG2 THR A 503 22747 23054 19374 5760 235 -1707 C
+ATOM 3678 N LYS A 504 64.865 91.071 -1.669 1.00141.41 N
+ANISOU 3678 N LYS A 504 17911 19106 16711 4058 -541 -2117 N
+ATOM 3679 CA LYS A 504 64.918 89.730 -2.251 1.00138.96 C
+ANISOU 3679 CA LYS A 504 17368 18711 16719 3706 -369 -1930 C
+ATOM 3680 C LYS A 504 66.335 89.382 -2.646 1.00142.04 C
+ANISOU 3680 C LYS A 504 17848 19062 17058 3520 -779 -2178 C
+ATOM 3681 O LYS A 504 66.762 88.230 -2.559 1.00134.46 O
+ANISOU 3681 O LYS A 504 16927 18053 16108 3463 -666 -2057 O
+ATOM 3682 CB LYS A 504 64.010 89.614 -3.477 1.00129.82 C
+ANISOU 3682 CB LYS A 504 15721 17488 16116 3223 -303 -1839 C
+ATOM 3683 CG LYS A 504 62.585 89.222 -3.164 1.00130.75 C
+ANISOU 3683 CG LYS A 504 15616 17544 16518 3307 225 -1458 C
+ATOM 3684 N LEU A 505 67.053 90.395 -3.100 1.00138.41 N
+ANISOU 3684 N LEU A 505 17394 18602 16593 3427 -1237 -2505 N
+ATOM 3685 CA LEU A 505 68.435 90.224 -3.458 1.00120.29 C
+ANISOU 3685 CA LEU A 505 15154 16230 14322 3285 -1619 -2726 C
+ATOM 3686 C LEU A 505 69.260 89.889 -2.223 1.00124.70 C
+ANISOU 3686 C LEU A 505 16126 16770 14484 3724 -1710 -2800 C
+ATOM 3687 O LEU A 505 70.166 89.052 -2.259 1.00124.02 O
+ANISOU 3687 O LEU A 505 16106 16619 14396 3643 -1808 -2823 O
+ATOM 3688 CB LEU A 505 68.966 91.499 -4.066 1.00109.42 C
+ANISOU 3688 CB LEU A 505 13673 14807 13094 3171 -2036 -3016 C
+ATOM 3689 CG LEU A 505 70.386 91.097 -4.404 1.00128.61 C
+ANISOU 3689 CG LEU A 505 16120 17111 15635 3034 -2336 -3157 C
+ATOM 3690 CD1 LEU A 505 70.509 91.048 -5.920 1.00141.22 C
+ANISOU 3690 CD1 LEU A 505 17393 18648 17616 2580 -2370 -3131 C
+ATOM 3691 CD2 LEU A 505 71.441 91.946 -3.655 1.00114.58 C
+ANISOU 3691 CD2 LEU A 505 14554 15224 13758 3350 -2784 -3462 C
+ATOM 3692 N LEU A 506 68.951 90.579 -1.132 1.00130.40 N
+ANISOU 3692 N LEU A 506 17159 17539 14847 4233 -1705 -2854 N
+ATOM 3693 CA LEU A 506 69.612 90.336 0.139 1.00131.63 C
+ANISOU 3693 CA LEU A 506 17798 17665 14549 4786 -1814 -2947 C
+ATOM 3694 C LEU A 506 69.501 88.865 0.507 1.00144.65 C
+ANISOU 3694 C LEU A 506 19548 19330 16080 4841 -1380 -2638 C
+ATOM 3695 O LEU A 506 70.448 88.287 1.024 1.00156.36 O
+ANISOU 3695 O LEU A 506 21304 20754 17351 5038 -1550 -2741 O
+ATOM 3696 CB LEU A 506 69.008 91.206 1.240 1.00120.17 C
+ANISOU 3696 CB LEU A 506 16713 16270 12675 5409 -1772 -2980 C
+ATOM 3697 N ARG A 507 68.351 88.260 0.214 1.00146.01 N
+ANISOU 3697 N ARG A 507 19470 19552 16453 4658 -839 -2263 N
+ATOM 3698 CA ARG A 507 68.159 86.831 0.443 1.00152.26 C
+ANISOU 3698 CA ARG A 507 20261 20320 17271 4649 -394 -1930 C
+ATOM 3699 C ARG A 507 69.164 86.004 -0.360 1.00145.14 C
+ANISOU 3699 C ARG A 507 19199 19352 16597 4200 -653 -2042 C
+ATOM 3700 O ARG A 507 69.471 84.873 0.007 1.00142.95 O
+ANISOU 3700 O ARG A 507 19044 19045 16224 4273 -450 -1882 O
+ATOM 3701 CB ARG A 507 66.724 86.401 0.111 1.00161.16 C
+ANISOU 3701 CB ARG A 507 21023 21434 18777 4463 165 -1523 C
+ATOM 3702 CG ARG A 507 65.661 86.975 1.046 1.00177.63 C
+ANISOU 3702 CG ARG A 507 23283 23565 20645 4978 585 -1290 C
+ATOM 3703 CD ARG A 507 64.263 86.468 0.696 1.00187.68 C
+ANISOU 3703 CD ARG A 507 24111 24757 22442 4769 1148 -857 C
+ATOM 3704 NE ARG A 507 63.229 87.082 1.527 1.00198.88 N
+ANISOU 3704 NE ARG A 507 25661 26202 23704 5259 1588 -600 N
+ATOM 3705 CZ ARG A 507 61.923 86.883 1.368 1.00205.71 C
+ANISOU 3705 CZ ARG A 507 26137 26967 25058 5169 2095 -210 C
+ATOM 3706 NH1 ARG A 507 61.484 86.084 0.406 1.00207.33 N
+ANISOU 3706 NH1 ARG A 507 25797 27020 25959 4610 2159 -75 N
+ATOM 3707 NH2 ARG A 507 61.055 87.485 2.171 1.00208.11 N
+ANISOU 3707 NH2 ARG A 507 26596 27293 25185 5668 2517 41 N
+ATOM 3708 N LEU A 508 69.681 86.579 -1.445 1.00134.19 N
+ANISOU 3708 N LEU A 508 17555 17933 15496 3776 -1072 -2294 N
+ATOM 3709 CA LEU A 508 70.654 85.888 -2.287 1.00125.06 C
+ANISOU 3709 CA LEU A 508 16259 16704 14555 3385 -1304 -2382 C
+ATOM 3710 C LEU A 508 72.070 85.983 -1.730 1.00133.75 C
+ANISOU 3710 C LEU A 508 17660 17739 15419 3609 -1705 -2655 C
+ATOM 3711 O LEU A 508 72.775 84.975 -1.650 1.00132.42 O
+ANISOU 3711 O LEU A 508 17581 17530 15202 3562 -1700 -2615 O
+ATOM 3712 CB LEU A 508 70.606 86.404 -3.726 1.00112.64 C
+ANISOU 3712 CB LEU A 508 14312 15095 13392 2907 -1513 -2482 C
+ATOM 3713 CG LEU A 508 69.271 86.186 -4.436 1.00113.17 C
+ANISOU 3713 CG LEU A 508 14056 15174 13769 2653 -1215 -2260 C
+ATOM 3714 CD1 LEU A 508 69.459 86.184 -5.945 1.00106.22 C
+ANISOU 3714 CD1 LEU A 508 12898 14225 13237 2216 -1432 -2343 C
+ATOM 3715 CD2 LEU A 508 68.613 84.894 -3.968 1.00117.32 C
+ANISOU 3715 CD2 LEU A 508 14560 15678 14341 2703 -779 -1932 C
+ATOM 3716 N SER A 509 72.491 87.188 -1.355 1.00130.72 N
+ANISOU 3716 N SER A 509 17414 17317 14936 3856 -2085 -2944 N
+ATOM 3717 CA SER A 509 73.767 87.347 -0.663 1.00136.66 C
+ANISOU 3717 CA SER A 509 18457 17948 15519 4156 -2531 -3236 C
+ATOM 3718 C SER A 509 73.698 86.583 0.646 1.00143.40 C
+ANISOU 3718 C SER A 509 19773 18845 15866 4687 -2319 -3138 C
+ATOM 3719 O SER A 509 74.680 85.977 1.082 1.00138.35 O
+ANISOU 3719 O SER A 509 19358 18121 15090 4839 -2521 -3256 O
+ATOM 3720 CB SER A 509 74.089 88.820 -0.410 1.00130.15 C
+ANISOU 3720 CB SER A 509 17685 17028 14738 4382 -3008 -3572 C
+ATOM 3721 OG SER A 509 74.991 89.319 -1.384 1.00125.27 O
+ANISOU 3721 OG SER A 509 16739 16248 14609 4003 -3376 -3749 O
+ATOM 3722 N SER A 510 72.520 86.615 1.263 1.00144.65 N
+ANISOU 3722 N SER A 510 20078 19123 15761 4999 -1878 -2899 N
+ATOM 3723 CA SER A 510 72.236 85.777 2.417 1.00148.97 C
+ANISOU 3723 CA SER A 510 21044 19713 15846 5526 -1487 -2677 C
+ATOM 3724 C SER A 510 72.424 84.315 2.046 1.00145.48 C
+ANISOU 3724 C SER A 510 20455 19266 15554 5204 -1182 -2426 C
+ATOM 3725 O SER A 510 73.001 83.552 2.811 1.00140.49 O
+ANISOU 3725 O SER A 510 20177 18606 14598 5539 -1145 -2415 O
+ATOM 3726 CB SER A 510 70.807 85.999 2.911 1.00149.05 C
+ANISOU 3726 CB SER A 510 21111 19824 15699 5832 -930 -2348 C
+ATOM 3727 OG SER A 510 70.346 84.882 3.643 1.00147.27 O
+ANISOU 3727 OG SER A 510 21097 19617 15240 6154 -337 -1962 O
+ATOM 3728 N SER A 511 71.946 83.946 0.858 1.00139.39 N
+ANISOU 3728 N SER A 511 19184 18508 15269 4583 -1004 -2249 N
+ATOM 3729 CA SER A 511 72.011 82.573 0.365 1.00129.68 C
+ANISOU 3729 CA SER A 511 17763 17254 14255 4236 -745 -2013 C
+ATOM 3730 C SER A 511 73.437 82.171 0.006 1.00129.30 C
+ANISOU 3730 C SER A 511 17762 17135 14232 4035 -1175 -2258 C
+ATOM 3731 O SER A 511 73.792 80.991 0.047 1.00109.17 O
+ANISOU 3731 O SER A 511 15254 14565 11659 3957 -1019 -2119 O
+ATOM 3732 CB SER A 511 71.108 82.416 -0.862 1.00125.40 C
+ANISOU 3732 CB SER A 511 16701 16703 14243 3684 -564 -1828 C
+ATOM 3733 OG SER A 511 71.167 81.106 -1.394 1.00137.08 O
+ANISOU 3733 OG SER A 511 17990 18125 15969 3359 -392 -1635 O
+ATOM 3734 N GLN A 512 74.247 83.164 -0.347 1.00131.12 N
+ANISOU 3734 N GLN A 512 17958 17304 14560 3957 -1699 -2603 N
+ATOM 3735 CA GLN A 512 75.621 82.941 -0.774 1.00120.52 C
+ANISOU 3735 CA GLN A 512 16587 15845 13361 3755 -2110 -2821 C
+ATOM 3736 C GLN A 512 76.508 82.796 0.431 1.00123.24 C
+ANISOU 3736 C GLN A 512 17385 16120 13322 4264 -2359 -3023 C
+ATOM 3737 O GLN A 512 77.569 82.174 0.385 1.00128.94 O
+ANISOU 3737 O GLN A 512 18162 16749 14081 4188 -2573 -3124 O
+ATOM 3738 CB GLN A 512 76.096 84.150 -1.546 1.00118.44 C
+ANISOU 3738 CB GLN A 512 16077 15483 13440 3537 -2531 -3073 C
+ATOM 3739 CG GLN A 512 76.798 83.822 -2.807 1.00125.91 C
+ANISOU 3739 CG GLN A 512 16711 16343 14787 3048 -2644 -3057 C
+ATOM 3740 CD GLN A 512 76.915 85.020 -3.690 1.00137.22 C
+ANISOU 3740 CD GLN A 512 17859 17690 16589 2843 -2877 -3186 C
+ATOM 3741 OE1 GLN A 512 77.456 86.052 -3.281 1.00153.03 O
+ANISOU 3741 OE1 GLN A 512 19904 19568 18672 3053 -3245 -3442 O
+ATOM 3742 NE2 GLN A 512 76.353 84.922 -4.897 1.00128.62 N
+ANISOU 3742 NE2 GLN A 512 16487 16643 15739 2470 -2678 -3017 N
+ATOM 3743 N GLY A 513 76.073 83.422 1.510 1.00128.93 N
+ANISOU 3743 N GLY A 513 18453 16869 13665 4826 -2362 -3100 N
+ATOM 3744 CA GLY A 513 76.767 83.309 2.761 1.00135.31 C
+ANISOU 3744 CA GLY A 513 19790 17602 14021 5449 -2610 -3308 C
+ATOM 3745 C GLY A 513 76.597 81.908 3.295 1.00133.10 C
+ANISOU 3745 C GLY A 513 19748 17398 13425 5620 -2132 -3010 C
+ATOM 3746 O GLY A 513 77.464 81.407 3.988 1.00135.48 O
+ANISOU 3746 O GLY A 513 20407 17622 13448 5952 -2344 -3163 O
+ATOM 3747 N THR A 514 75.478 81.270 2.971 1.00130.00 N
+ANISOU 3747 N THR A 514 19139 17128 13128 5402 -1499 -2584 N
+ATOM 3748 CA THR A 514 75.252 79.899 3.409 1.00136.05 C
+ANISOU 3748 CA THR A 514 20053 17932 13707 5525 -990 -2248 C
+ATOM 3749 C THR A 514 76.125 78.980 2.571 1.00136.91 C
+ANISOU 3749 C THR A 514 19914 17993 14111 4991 -1151 -2279 C
+ATOM 3750 O THR A 514 76.451 77.859 2.971 1.00136.85 O
+ANISOU 3750 O THR A 514 20093 17981 13923 5102 -944 -2139 O
+ATOM 3751 CB THR A 514 73.784 79.475 3.234 1.00141.83 C
+ANISOU 3751 CB THR A 514 20522 18734 14631 5408 -287 -1768 C
+ATOM 3752 OG1 THR A 514 73.591 78.921 1.927 1.00142.93 O
+ANISOU 3752 OG1 THR A 514 20113 18858 15336 4676 -233 -1640 O
+ATOM 3753 CG2 THR A 514 72.861 80.659 3.413 1.00145.09 C
+ANISOU 3753 CG2 THR A 514 20916 19192 15018 5620 -214 -1761 C
+ATOM 3754 N ILE A 515 76.491 79.473 1.394 1.00129.08 N
+ANISOU 3754 N ILE A 515 18518 16960 13565 4442 -1494 -2442 N
+ATOM 3755 CA ILE A 515 77.327 78.735 0.468 1.00119.39 C
+ANISOU 3755 CA ILE A 515 17053 15677 12633 3951 -1657 -2465 C
+ATOM 3756 C ILE A 515 78.787 78.796 0.895 1.00127.05 C
+ANISOU 3756 C ILE A 515 18275 16524 13475 4143 -2161 -2798 C
+ATOM 3757 O ILE A 515 79.482 77.778 0.906 1.00128.44 O
+ANISOU 3757 O ILE A 515 18530 16671 13600 4065 -2153 -2760 O
+ATOM 3758 CB ILE A 515 77.220 79.308 -0.945 1.00110.42 C
+ANISOU 3758 CB ILE A 515 15452 14516 11987 3401 -1815 -2500 C
+ATOM 3759 CG1 ILE A 515 75.801 79.150 -1.481 1.00109.39 C
+ANISOU 3759 CG1 ILE A 515 15038 14466 12060 3177 -1388 -2203 C
+ATOM 3760 CG2 ILE A 515 78.168 78.587 -1.861 1.00112.80 C
+ANISOU 3760 CG2 ILE A 515 15581 14743 12533 2997 -1979 -2516 C
+ATOM 3761 CD1 ILE A 515 75.570 79.879 -2.780 1.00110.01 C
+ANISOU 3761 CD1 ILE A 515 14740 14519 12538 2759 -1561 -2268 C
+ATOM 3762 N GLU A 516 79.240 79.996 1.247 1.00122.76 N
+ANISOU 3762 N GLU A 516 17837 15878 12927 4400 -2627 -3132 N
+ATOM 3763 CA GLU A 516 80.636 80.218 1.589 1.00124.18 C
+ANISOU 3763 CA GLU A 516 18172 15860 13149 4571 -3208 -3493 C
+ATOM 3764 C GLU A 516 81.099 79.274 2.681 1.00126.09 C
+ANISOU 3764 C GLU A 516 18894 16095 12918 5029 -3183 -3522 C
+ATOM 3765 O GLU A 516 82.117 78.595 2.539 1.00116.84 O
+ANISOU 3765 O GLU A 516 17721 14825 11848 4893 -3381 -3605 O
+ATOM 3766 CB GLU A 516 80.863 81.656 2.046 1.00135.21 C
+ANISOU 3766 CB GLU A 516 19658 17112 14603 4907 -3722 -3854 C
+ATOM 3767 CG GLU A 516 82.315 82.045 1.962 1.00146.41 C
+ANISOU 3767 CG GLU A 516 20992 18238 16400 4885 -4381 -4215 C
+ATOM 3768 CD GLU A 516 82.865 81.775 0.582 1.00151.28 C
+ANISOU 3768 CD GLU A 516 21100 18789 17590 4220 -4329 -4073 C
+ATOM 3769 OE1 GLU A 516 82.373 82.413 -0.367 1.00146.52 O
+ANISOU 3769 OE1 GLU A 516 20133 18221 17316 3867 -4198 -3957 O
+ATOM 3770 OE2 GLU A 516 83.763 80.917 0.441 1.00154.24 O
+ANISOU 3770 OE2 GLU A 516 21471 19078 18055 4089 -4397 -4065 O
+END
--- /dev/null
+HEADER TRANSFERASE/TRANSFERASE INHIBITOR 01-JAN-13 4IM2
+TITLE STRUCTURE OF TANK-BINDING KINASE 1 (Truncated test file)
+DBREF 4IM2 A 1 657 UNP Q9UHD2 TBK1_HUMAN 1 657
+SEQADV 4IM2 GLY A -5 UNP Q9UHD2 EXPRESSION TAG
+SEQADV 4IM2 SER A -4 UNP Q9UHD2 EXPRESSION TAG
+SEQADV 4IM2 GLY A -3 UNP Q9UHD2 EXPRESSION TAG
+SEQADV 4IM2 SER A -2 UNP Q9UHD2 EXPRESSION TAG
+SEQADV 4IM2 GLY A -1 UNP Q9UHD2 EXPRESSION TAG
+SEQADV 4IM2 SER A 0 UNP Q9UHD2 EXPRESSION TAG
+SEQRES 1 A 663 GLY SER GLY SER GLY SER MET GLN SER THR SER ASN HIS
+ATOM 1 N GLY A -1 126.784 4.226 -23.353 1.00158.13 N
+ANISOU 1 N GLY A -1 19370 17517 23197 6628 1162 2075 N
+ATOM 2 CA GLY A -1 125.521 4.306 -24.062 1.00150.94 C
+ANISOU 2 CA GLY A -1 18746 16231 22374 6153 1277 1996 C
+ATOM 3 C GLY A -1 125.742 4.361 -25.557 1.00146.29 C
+ANISOU 3 C GLY A -1 18187 15453 21943 5900 1405 1498 C
+ATOM 4 O GLY A -1 126.691 4.980 -26.029 1.00150.85 O
+ANISOU 4 O GLY A -1 18536 16366 22413 5906 1385 1160 O
+ATOM 5 N SER A 0 124.869 3.710 -26.313 1.00137.36 N
+ANISOU 5 N SER A 0 17328 13796 21068 5675 1550 1432 N
+ATOM 6 CA SER A 0 125.052 3.672 -27.755 1.00139.44 C
+ANISOU 6 CA SER A 0 17634 13884 21461 5464 1674 953 C
+ATOM 7 C SER A 0 123.846 4.104 -28.574 1.00137.43 C
+ANISOU 7 C SER A 0 17591 13478 21149 4975 1714 755 C
+ATOM 8 O SER A 0 122.737 4.275 -28.071 1.00128.25 O
+ANISOU 8 O SER A 0 16566 12244 19921 4780 1667 988 O
+ATOM 9 CB SER A 0 125.578 2.312 -28.214 1.00155.09 C
+ANISOU 9 CB SER A 0 19671 15395 23862 5752 1827 887 C
+ATOM 10 OG SER A 0 126.993 2.281 -28.131 1.00164.59 O
+ANISOU 10 OG SER A 0 20608 16866 25062 6113 1802 781 O
+ATOM 11 N MET A 1 124.096 4.270 -29.861 1.00134.87 N
+ANISOU 11 N MET A 1 17283 13123 20839 4799 1805 311 N
+ATOM 12 CA MET A 1 123.214 5.039 -30.698 1.00125.22 C
+ANISOU 12 CA MET A 1 16193 11958 19428 4369 1804 70 C
+ATOM 13 C MET A 1 122.885 4.351 -32.006 1.00124.69 C
+ANISOU 13 C MET A 1 16293 11510 19572 4225 1942 -293 C
+ATOM 14 O MET A 1 123.723 3.686 -32.606 1.00129.61 O
+ANISOU 14 O MET A 1 16868 11984 20394 4414 2057 -519 O
+ATOM 15 CB MET A 1 123.867 6.392 -30.970 1.00122.51 C
+ANISOU 15 CB MET A 1 15675 12140 18732 4254 1762 -132 C
+ATOM 16 CG MET A 1 125.074 6.368 -31.866 1.00120.74 C
+ANISOU 16 CG MET A 1 15318 12013 18544 4369 1884 -495 C
+ATOM 17 SD MET A 1 125.834 7.982 -31.850 1.00196.33 S
+ANISOU 17 SD MET A 1 24655 22193 27747 4246 1861 -642 S
+ATOM 18 CE MET A 1 126.785 7.896 -30.345 1.00132.53 C
+ANISOU 18 CE MET A 1 16264 14397 19693 4639 1728 -355 C
+ATOM 19 N GLN A 2 121.643 4.496 -32.440 1.00123.78 N
+ANISOU 19 N GLN A 2 16363 11253 19416 3898 1925 -369 N
+ATOM 20 CA GLN A 2 121.313 4.161 -33.809 1.00128.51 C
+ANISOU 20 CA GLN A 2 17093 11643 20094 3714 2020 -799 C
+ATOM 21 C GLN A 2 121.639 5.396 -34.617 1.00121.06 C
+ANISOU 21 C GLN A 2 16105 11138 18752 3541 2004 -1065 C
+ATOM 22 O GLN A 2 121.959 6.442 -34.059 1.00107.32 O
+ANISOU 22 O GLN A 2 14247 9790 16739 3528 1928 -906 O
+ATOM 23 CB GLN A 2 119.832 3.845 -33.965 1.00136.11 C
+ANISOU 23 CB GLN A 2 18240 12314 21161 3439 1994 -809 C
+ATOM 24 CG GLN A 2 119.171 3.277 -32.740 1.00148.45 C
+ANISOU 24 CG GLN A 2 19841 13613 22949 3500 1973 -376 C
+ATOM 25 CD GLN A 2 117.773 2.799 -33.042 1.00158.28 C
+ANISOU 25 CD GLN A 2 21243 14511 24385 3221 1993 -473 C
+ATOM 26 OE1 GLN A 2 116.827 3.097 -32.313 1.00163.28 O
+ANISOU 26 OE1 GLN A 2 21915 15160 24966 3070 1921 -211 O
+ATOM 27 NE2 GLN A 2 117.631 2.057 -34.134 1.00155.02 N
+ANISOU 27 NE2 GLN A 2 20902 13797 24200 3144 2095 -885 N
+ATOM 28 N SER A 3 121.547 5.280 -35.931 1.00124.66 N
+ANISOU 28 N SER A 3 16661 11530 19175 3410 2090 -1474 N
+ATOM 29 CA SER A 3 121.742 6.432 -36.781 1.00120.35 C
+ANISOU 29 CA SER A 3 16121 11369 18236 3242 2107 -1703 C
+ATOM 30 C SER A 3 121.190 6.186 -38.161 1.00125.27 C
+ANISOU 30 C SER A 3 16914 11882 18801 3073 2165 -2108 C
+ATOM 31 O SER A 3 120.746 5.090 -38.489 1.00135.86 O
+ANISOU 31 O SER A 3 18337 12848 20436 3082 2197 -2268 O
+ATOM 32 CB SER A 3 123.217 6.751 -36.923 1.00116.70 C
+ANISOU 32 CB SER A 3 15475 11153 17711 3435 2220 -1807 C
+ATOM 33 OG SER A 3 123.770 5.974 -37.974 1.00112.78 O
+ANISOU 33 OG SER A 3 15005 10478 17367 3528 2375 -2175 O
+ATOM 34 N THR A 4 121.244 7.232 -38.972 1.00116.48 N
+ANISOU 34 N THR A 4 15849 11109 17301 2928 2191 -2281 N
+ATOM 35 CA THR A 4 120.978 7.130 -40.394 1.00113.12 C
+ANISOU 35 CA THR A 4 15568 10691 16723 2823 2262 -2692 C
+ATOM 36 C THR A 4 122.118 7.839 -41.119 1.00116.32 C
+ANISOU 36 C THR A 4 15918 11410 16867 2884 2432 -2867 C
+ATOM 37 O THR A 4 123.106 8.236 -40.495 1.00117.17 O
+ANISOU 37 O THR A 4 15851 11671 16998 3007 2493 -2706 O
+ATOM 38 CB THR A 4 119.615 7.756 -40.775 1.00106.20 C
+ANISOU 38 CB THR A 4 14854 9927 15568 2568 2121 -2713 C
+ATOM 39 OG1 THR A 4 119.774 9.154 -41.043 1.00107.14 O
+ANISOU 39 OG1 THR A 4 15001 10451 15258 2480 2138 -2644 O
+ATOM 40 CG2 THR A 4 118.597 7.567 -39.657 1.00 99.42 C
+ANISOU 40 CG2 THR A 4 13990 8889 14896 2483 1956 -2396 C
+ATOM 41 N SER A 5 121.981 7.982 -42.432 1.00116.70 N
+ANISOU 41 N SER A 5 16106 11564 16670 2803 2517 -3210 N
+ATOM 42 CA SER A 5 122.975 8.671 -43.247 1.00122.60 C
+ANISOU 42 CA SER A 5 16837 12604 17144 2839 2721 -3385 C
+ATOM 43 C SER A 5 123.317 10.064 -42.713 1.00128.43 C
+ANISOU 43 C SER A 5 17501 13666 17630 2768 2748 -3105 C
+ATOM 44 O SER A 5 124.481 10.467 -42.712 1.00133.01 O
+ANISOU 44 O SER A 5 17934 14410 18193 2852 2925 -3133 O
+ATOM 45 CB SER A 5 122.473 8.779 -44.687 1.00127.34 C
+ANISOU 45 CB SER A 5 17646 13318 17418 2741 2774 -3729 C
+ATOM 46 OG SER A 5 121.108 9.163 -44.712 1.00135.31 O
+ANISOU 46 OG SER A 5 18807 14370 18235 2568 2576 -3643 O
+ATOM 47 N ASN A 6 122.303 10.783 -42.240 1.00122.78 N
+ANISOU 47 N ASN A 6 16868 13033 16750 2608 2581 -2859 N
+ATOM 48 CA ASN A 6 122.460 12.194 -41.897 1.00114.44 C
+ANISOU 48 CA ASN A 6 15777 12275 15429 2507 2620 -2639 C
+ATOM 49 C ASN A 6 122.348 12.537 -40.412 1.00108.55 C
+ANISOU 49 C ASN A 6 14870 11544 14832 2498 2474 -2282 C
+ATOM 50 O ASN A 6 122.712 13.640 -40.004 1.00110.16 O
+ANISOU 50 O ASN A 6 14983 11984 14890 2435 2531 -2135 O
+ATOM 51 CB ASN A 6 121.461 13.034 -42.695 1.00113.00 C
+ANISOU 51 CB ASN A 6 15832 12254 14850 2339 2583 -2658 C
+ATOM 52 CG ASN A 6 121.646 12.886 -44.191 1.00118.14 C
+ANISOU 52 CG ASN A 6 16648 12982 15257 2366 2743 -2999 C
+ATOM 53 OD1 ASN A 6 122.765 12.952 -44.698 1.00122.16 O
+ANISOU 53 OD1 ASN A 6 17097 13580 15737 2449 2985 -3154 O
+ATOM 54 ND2 ASN A 6 120.546 12.672 -44.905 1.00118.96 N
+ANISOU 54 ND2 ASN A 6 16946 13074 15179 2302 2609 -3139 N
+ATOM 55 N HIS A 7 121.845 11.605 -39.608 1.00100.48 N
+ANISOU 55 N HIS A 7 13810 10269 14098 2560 2305 -2149 N
+ATOM 56 CA HIS A 7 121.657 11.871 -38.183 1.00 91.49 C
+ANISOU 56 CA HIS A 7 12535 9160 13066 2569 2162 -1799 C
+ATOM 57 C HIS A 7 122.134 10.725 -37.300 1.00 97.74 C
+ANISOU 57 C HIS A 7 13180 9725 14232 2793 2117 -1685 C
+ATOM 58 O HIS A 7 122.456 9.647 -37.791 1.00101.23 O
+ANISOU 58 O HIS A 7 13643 9923 14898 2924 2188 -1876 O
+ATOM 59 CB HIS A 7 120.189 12.175 -37.884 1.00 86.30 C
+ANISOU 59 CB HIS A 7 12021 8464 12306 2383 1977 -1628 C
+ATOM 60 CG HIS A 7 119.634 13.303 -38.694 1.00101.46 C
+ANISOU 60 CG HIS A 7 14094 10603 13853 2201 2000 -1699 C
+ATOM 61 ND1 HIS A 7 119.265 13.157 -40.015 1.00 99.83 N
+ANISOU 61 ND1 HIS A 7 14076 10384 13472 2153 2049 -1976 N
+ATOM 62 CD2 HIS A 7 119.401 14.600 -38.379 1.00 89.60 C
+ANISOU 62 CD2 HIS A 7 12588 9342 12114 2078 1988 -1527 C
+ATOM 63 CE1 HIS A 7 118.823 14.314 -40.476 1.00 97.86 C
+ANISOU 63 CE1 HIS A 7 13944 10363 12875 2029 2062 -1939 C
+ATOM 64 NE2 HIS A 7 118.896 15.206 -39.503 1.00 93.14 N
+ANISOU 64 NE2 HIS A 7 13235 9899 12253 1975 2035 -1667 N
+END
--- /dev/null
+HMMER3/f [3.1b2 | February 2015]
+NAME uniref50
+LENG 148
+ALPH amino
+ RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Mon Jun 12 14:32:05 2017
+NSEQ 15
+EFFN 0.648193
+CKSUM 2563184735
+STATS LOCAL MSV -10.0682 0.70956
+STATS LOCAL VITERBI -10.7870 0.70956
+STATS LOCAL FORWARD -4.6837 0.70956
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.40816 3.71583 2.80837 2.63551 3.47092 2.77036 3.85028 2.88279 2.80267 2.53589 3.68425 3.22102 3.34428 3.14560 3.11474 2.53177 2.75990 2.58070 5.00144 3.51101
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.10433 3.97705 2.52157 0.61958 0.77255 0.00000 *
+ 1 2.99317 4.53706 4.08224 3.67789 3.22093 3.85692 4.40592 2.39958 3.44433 1.81088 1.32037 3.95163 4.31759 3.82413 3.64608 3.34553 3.29902 2.40928 5.06591 3.83044 1 m - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 2 0.97044 4.20710 3.49350 3.28598 4.08269 3.03087 4.30444 3.21278 3.30302 3.09300 4.12129 3.42792 3.77296 3.64134 3.55157 2.55705 2.83652 2.86187 5.50678 4.31039 2 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.11955 3.90315 2.38048 0.61958 0.77255 0.55549 0.85282
+ 3 1.74035 4.09199 3.34495 3.00819 4.05288 2.91638 4.05509 3.33461 3.01251 3.11462 3.97728 3.20348 3.62940 3.32849 3.32799 1.99191 1.99086 2.89563 5.42641 4.20726 3 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03323 3.81683 4.53917 0.61958 0.77255 0.62561 0.76558
+ 4 2.37663 4.18625 3.55838 3.17855 3.75132 3.18264 4.13666 2.64341 3.07328 2.62344 3.69712 3.39774 3.83139 3.44405 3.35689 2.61052 1.64486 2.15973 5.30034 4.05468 4 t - - -
+ 2.68617 4.42230 2.77525 2.73129 3.46359 2.40511 3.72500 3.29359 2.67746 2.69350 4.24695 2.90352 2.73719 3.18152 2.89806 2.37885 2.77501 2.98524 4.58482 3.61508
+ 0.33937 1.47682 2.82312 0.71438 0.67236 0.50642 0.92294
+ 5 1.78828 4.31568 3.18846 2.75366 3.97645 3.11838 3.84000 3.34055 2.67250 3.02453 3.87541 3.10729 3.71676 3.06391 2.67828 2.15246 2.50645 2.96422 5.30410 4.05011 9 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322
+ 6 2.60146 4.34120 4.20318 3.64233 3.23200 4.03946 4.38229 1.91078 3.53317 1.46276 2.80385 3.95250 4.35454 3.78680 3.77614 3.34686 3.12310 1.90138 5.05979 3.90282 10 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322
+ 7 2.51618 4.38929 3.20785 2.68482 3.53842 3.39630 3.71025 2.97988 2.63127 2.66315 3.23915 3.11866 3.35060 2.98059 3.01133 2.11689 2.77574 2.72369 4.95633 3.10650 11 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03188 3.85742 4.57976 0.61958 0.77255 0.59400 0.80322
+ 8 1.83112 4.12334 3.20156 2.95461 4.23963 1.79514 4.09699 3.64646 3.07597 3.33878 4.16582 3.16397 3.61350 3.35846 3.40724 1.96001 2.64648 3.10558 5.57497 4.34818 12 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.07518 3.85742 2.97012 0.61958 0.77255 0.59400 0.80322
+ 9 2.02467 4.19921 3.47207 3.00878 3.03795 3.27081 3.95597 2.70270 2.96218 2.55248 3.54468 3.31239 3.83177 3.27950 3.28895 2.63385 2.09090 2.46488 5.06606 3.80489 13 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03327 3.81551 4.53786 0.61958 0.77255 0.56041 0.84624
+ 10 2.25155 4.19461 3.85704 3.29295 2.92371 3.72128 4.04839 2.07964 3.20853 2.08962 2.71310 3.60847 4.09120 3.47607 3.47945 3.00735 2.74040 2.14097 4.86082 3.65928 14 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03170 3.86316 4.58551 0.61958 0.77255 0.53107 0.88667
+ 11 2.97746 4.34766 4.53309 3.96552 2.78843 4.21079 4.53997 1.80103 3.85948 1.59494 2.57669 4.20401 4.48099 4.02954 4.02513 3.53069 3.20806 1.63119 5.03312 3.89134 15 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 12 2.01604 4.15364 3.23013 2.99255 4.26101 2.66741 4.12859 3.66796 3.09383 3.37186 4.20680 3.19709 3.64453 3.39377 3.41395 1.27425 2.68165 3.13093 5.59931 4.36607 16 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 13 2.41396 4.26265 3.40226 2.93569 3.72492 3.24366 3.92462 2.93397 2.83929 2.73560 3.16052 3.25846 3.81309 3.20648 3.16819 2.37913 1.73294 2.65776 5.16309 3.91530 17 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 14 2.06589 4.14828 3.30608 3.02868 4.20053 2.92394 4.12227 3.52677 3.06750 3.27902 4.13704 3.22373 3.65849 3.38850 3.37961 1.31011 2.40891 3.04032 5.55736 4.32788 18 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 15 2.74009 4.29274 3.92243 3.42912 1.74599 3.72053 3.90473 2.32427 3.32349 2.18956 3.31553 3.65797 4.14118 3.57919 3.55745 2.71376 3.01017 2.38146 4.46330 2.97696 19 f - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 16 2.76094 4.39380 4.31945 3.75589 3.18422 4.12530 4.45889 2.01307 3.63847 1.30728 2.59228 4.05575 4.41925 3.86957 3.85970 3.43754 3.19324 1.94550 5.06650 3.93230 20 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 17 2.70295 4.73637 3.16526 2.68917 4.18427 3.37581 3.71759 3.61851 2.27125 3.18722 4.06871 3.11427 2.39752 2.89725 1.66361 2.77186 2.98335 3.28411 5.34221 4.10051 21 r - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.07762 3.90315 2.90945 0.61958 0.77255 0.55549 0.85282
+ 18 2.49055 4.81399 3.14505 2.59164 4.19520 3.44406 3.60132 3.55142 1.92611 3.12799 3.98038 3.04037 3.86298 2.75679 1.83484 2.76119 2.76042 3.23493 5.31169 4.06564 22 r - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.06501 3.85742 3.17445 0.61958 0.77255 0.59400 0.80322
+ 19 2.43450 4.81939 2.81703 2.39298 4.15804 3.33308 3.59871 3.56807 2.06609 3.14527 3.97247 2.89702 3.36070 2.29211 2.66793 2.54254 2.87166 3.22778 5.35034 4.03520 23 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03294 3.82535 4.54770 0.61958 0.77255 0.61916 0.77305
+ 20 2.61608 4.67386 2.79167 2.51004 4.07010 3.23635 3.73836 3.55025 2.48903 3.13320 4.04098 2.97430 2.02723 2.34075 2.83811 2.68076 2.93097 3.21608 5.34739 4.03735 24 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03294 3.82535 4.54770 0.61958 0.77255 0.51069 0.91649
+ 21 1.83080 4.22890 3.60014 3.08598 3.61014 3.38577 4.01761 2.55536 3.00939 2.52819 3.20189 3.39791 3.91288 3.33215 3.33591 2.72706 2.41446 2.12040 5.12303 3.89826 25 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 22 2.43845 4.29437 3.39983 3.04145 3.80350 3.19872 4.06195 2.96220 2.98493 2.76612 3.80233 3.32666 1.71751 3.35496 3.29387 2.63325 2.83846 2.21304 5.28839 4.02321 26 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 23 2.55648 4.28453 3.47615 2.92649 3.45346 3.51308 3.86072 2.37030 2.85167 2.40896 2.93550 3.31525 2.97437 3.17776 3.19434 2.79032 2.33896 2.42929 4.94762 3.71651 27 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 24 2.23005 4.31546 3.25841 2.77512 3.78441 3.22479 3.82985 3.12652 2.73582 2.83244 3.03171 3.14960 3.26067 3.07830 3.10838 1.85715 2.73859 2.81468 5.16957 3.91289 28 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 25 2.72216 3.51794 4.14734 3.58168 3.26953 3.85722 4.23682 2.10046 3.47012 1.71220 2.91412 3.83361 4.22096 3.71804 3.68973 3.16541 2.79579 1.71693 4.93656 3.75086 29 l - - -
+ 2.68606 4.42227 2.77522 2.73126 3.46337 2.40515 3.72497 3.29356 2.67743 2.69357 4.24692 2.90349 2.73742 3.18149 2.89784 2.37889 2.77522 2.98521 4.58479 3.61506
+ 0.31572 1.55442 2.82310 0.27619 1.42159 0.55549 0.85282
+ 26 2.06718 4.47388 3.00085 2.59301 4.03403 3.18938 3.75234 3.40130 2.21691 3.06406 3.90876 3.01767 3.74194 2.94856 2.91976 2.09488 2.60568 3.04014 5.32541 4.04568 31 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03205 3.85226 4.57460 0.61958 0.77255 0.52495 0.89548
+ 27 2.09937 4.25808 3.35967 2.86682 3.65405 3.28224 3.85971 2.93650 2.81278 2.15397 3.59474 3.22143 3.43624 3.14697 3.16235 2.43009 2.43628 2.66078 5.07593 3.83686 32 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 28 2.56380 4.32380 3.45039 2.92280 3.52453 3.48960 3.88793 2.33272 2.83649 2.29194 3.45598 3.31192 2.56007 3.18425 3.18050 2.78603 2.52825 2.43071 5.02605 3.78340 33 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 29 2.52137 4.41862 3.18708 2.64701 3.24265 3.41116 3.70401 2.99879 2.50849 2.54033 3.56040 3.09794 3.19241 2.94883 3.00442 2.32271 2.53579 2.73855 5.01724 3.74765 34 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 30 2.00013 4.58033 2.94855 2.53646 4.07584 3.24271 3.72285 3.46598 2.50253 3.10366 3.94143 2.28591 3.76727 2.90505 2.65085 2.58556 2.61842 3.10852 5.34830 4.05040 35 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 31 2.38233 4.27978 3.41241 2.86526 3.23400 3.48475 3.81694 2.67786 2.81404 2.37039 3.42629 2.84230 3.90072 3.13098 3.17039 2.75440 2.50322 2.16090 4.92926 3.68461 36 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 32 2.57741 4.71210 2.95136 2.48036 4.10354 2.51445 3.64563 3.50876 2.11219 3.10615 3.93363 2.96219 3.79067 2.80786 2.54902 2.50592 2.51289 3.16566 5.32824 4.02677 37 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 33 2.48649 4.79372 2.91636 2.20828 4.05411 3.38774 3.59403 3.46081 2.32653 3.05709 3.87988 2.78811 3.79502 2.48988 2.50461 2.63652 2.83744 2.71303 5.28703 3.96685 38 e - - -
+ 2.68619 4.42226 2.77520 2.73124 3.46338 2.40514 3.72495 3.29355 2.67742 2.69356 4.24691 2.90348 2.73732 3.18147 2.89802 2.37888 2.77520 2.98519 4.58478 3.61504
+ 0.07101 2.83445 4.62550 0.63888 0.75053 0.55549 0.85282
+ 34 1.61247 4.12982 3.30077 3.01153 4.23531 2.30721 4.11812 3.64225 3.09602 3.33089 4.15414 3.20546 3.63382 3.37908 3.42786 1.71494 2.65404 3.10635 5.57312 4.35188 41 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 35 2.72153 4.23229 3.98871 3.42694 2.97156 3.37228 4.12428 2.11066 3.32720 1.56866 3.14804 3.72158 4.17041 3.58506 3.57523 3.10753 2.96236 2.01957 4.85619 3.63474 42 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 36 2.59948 4.33296 4.13320 3.58598 1.90470 3.92561 4.14661 2.31847 3.46961 1.74381 2.73954 3.84829 4.26638 3.69996 3.68809 3.23462 3.08833 2.27549 4.71854 3.39100 43 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 37 2.58931 4.58161 2.85848 2.66250 4.27569 1.35942 3.92193 3.72667 2.37699 3.36968 4.25453 3.08080 3.80217 3.15095 3.05968 2.68693 2.97358 3.32002 5.50315 4.25822 44 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 38 2.65443 4.41996 3.43781 2.92526 3.49579 3.52457 3.83449 2.83057 2.64507 1.65492 3.47551 3.30970 3.36731 3.12885 2.65176 2.85231 2.91346 2.65496 4.98654 3.73087 45 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 39 2.72350 4.79628 3.09209 2.60253 4.10688 3.43694 3.64699 3.48037 1.53491 2.80300 3.97997 3.05455 3.87955 2.81812 2.48623 2.53142 2.96661 3.17965 5.30004 4.01932 46 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 40 1.82674 4.13179 3.37396 3.04098 4.15468 2.93287 4.10316 3.48191 3.05943 3.22685 4.07364 3.23234 3.65478 3.36800 3.38156 1.54612 2.23418 3.00585 5.51189 4.29184 47 s - - -
+ 2.68618 4.42225 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37887 2.77520 2.98508 4.58477 3.61503
+ 0.07101 2.83445 4.62550 0.49418 0.94179 0.55549 0.85282
+ 41 1.87334 4.14690 3.25058 2.97809 4.26468 2.12605 4.11046 3.68104 3.08263 3.36184 4.18261 3.18779 3.63442 3.36584 3.42015 1.58161 2.66271 3.13490 5.59481 4.36766 49 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.11955 3.90315 2.38048 0.61958 0.77255 0.55549 0.85282
+ 42 2.21070 4.25592 3.22113 2.77420 3.85340 3.11965 3.84389 3.18555 2.74438 2.69874 3.77079 3.12117 3.16635 3.08826 3.10948 2.13243 2.17697 2.83916 5.22265 3.97074 50 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03323 3.81683 4.53917 0.61958 0.77255 0.62561 0.76558
+ 43 2.34367 4.62113 3.10732 2.54725 3.88271 3.41056 3.61301 3.25335 2.12788 2.89080 3.32993 3.01581 3.81452 2.79680 2.35592 2.55841 2.82420 2.96607 5.15612 3.88260 51 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.07842 3.81683 2.92953 0.61958 0.77255 0.50642 0.92294
+ 44 2.82371 4.84862 3.20218 2.72371 4.21308 3.44211 3.65714 3.71157 2.07944 3.25434 4.14899 2.84303 3.91564 2.83614 1.36807 2.87376 3.07618 3.38687 5.31229 4.06004 52 r - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.12129 3.86316 2.37274 0.61958 0.77255 0.58934 0.80899
+ 45 2.50307 4.57358 2.77436 2.48515 4.13002 2.10145 3.72113 3.58708 2.48196 3.19739 4.04544 2.56817 3.72971 2.91621 2.54565 2.57756 2.84032 3.19983 5.38083 4.07634 53 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03462 3.77648 4.49883 0.61958 0.77255 0.55399 0.85485
+ 46 2.68547 4.96255 2.09111 2.21584 4.36925 1.97687 3.70446 3.84410 2.62382 3.41713 4.25934 2.75900 3.76266 2.58919 3.12019 2.66938 2.98839 3.45462 5.60805 4.21173 54 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03205 3.85226 4.57460 0.61958 0.77255 0.52495 0.89548
+ 47 2.70472 4.70735 3.22145 2.64799 3.96742 3.15410 3.63371 3.33902 2.12091 2.43520 3.82970 3.09240 3.88741 2.81708 1.91192 2.78290 2.92703 3.06076 5.19463 3.94224 55 r - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 48 2.39251 4.23853 3.75245 3.18839 3.35715 3.69117 4.01036 2.17738 3.07061 2.00722 3.28706 3.53429 4.07078 3.39072 3.07752 2.97399 2.89120 1.85844 4.92824 3.71532 56 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 49 2.56050 4.39105 3.34411 2.78319 3.60155 3.46480 3.77128 2.83822 2.62742 2.58594 3.21262 3.20237 3.88486 3.03059 2.56448 2.73642 2.19035 2.37832 5.02624 3.77891 57 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 50 1.37812 2.80072 3.83498 3.42070 3.87397 2.99921 4.24161 2.96530 3.32256 2.89459 3.81917 3.44880 3.71764 3.60422 3.56604 2.43360 2.40411 2.61888 5.33835 4.15246 58 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.55549 0.85282
+ 51 2.74532 4.50724 3.42983 2.95244 3.42568 3.60626 3.88910 2.77026 2.70375 2.22807 1.95486 3.35569 4.02547 2.58121 2.99178 2.94186 2.99694 2.66631 5.01046 3.74777 59 m - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03044 3.90315 4.62550 0.61958 0.77255 0.44450 1.02483
+ 52 0.87297 4.24657 3.57075 3.36786 4.15839 3.06811 4.37727 3.29971 3.38685 3.17640 4.19749 3.49040 3.81731 3.71861 3.62959 2.59634 2.88098 2.93600 5.57511 4.38724 60 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 53 1.96298 4.17134 3.43460 3.07855 4.14627 2.98936 4.12481 3.46945 3.08161 3.21642 4.06614 3.27556 3.70074 3.39215 3.40515 1.84467 1.63498 3.01250 5.50977 4.28998 61 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 54 3.40066 4.84720 3.99369 3.74344 2.30278 3.95279 3.67128 3.39553 3.59798 2.82228 4.05988 3.85394 4.42456 3.87882 3.75994 3.52665 3.68805 3.27113 3.95029 0.80817 62 y - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 55 2.86663 5.06853 2.87640 2.51952 4.45748 3.43879 3.66568 3.89866 1.33937 3.41664 4.27179 2.44223 3.91577 2.81805 2.46217 2.85914 3.10555 3.54515 5.50478 4.21799 63 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 56 2.89101 4.40561 4.26922 3.93641 3.62800 3.83108 4.72052 2.04974 3.80577 2.29743 3.57810 4.10920 4.38636 4.15841 4.00806 3.34183 3.25039 0.90272 5.42983 4.16757 64 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 57 2.78989 4.87427 3.10728 2.66228 4.33471 3.44160 3.70636 3.64306 1.30828 3.25641 4.14609 3.10047 3.92071 2.86764 2.46119 2.83588 2.59339 3.32217 5.44317 4.19498 65 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 58 3.28295 4.64373 4.65267 4.15432 2.12281 4.39226 4.40565 2.30868 4.01063 0.99404 2.96208 4.34589 4.63887 4.13687 4.14117 3.75853 3.51440 2.42033 4.68321 3.26182 66 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 59 3.08248 4.42168 4.72065 4.23378 3.50231 4.37831 4.95293 1.13074 4.10572 1.99571 3.31982 4.46032 4.70821 4.37869 4.30619 3.77127 3.35421 1.44848 5.47660 4.27063 67 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 60 2.47137 4.31634 3.52340 3.28135 4.06362 3.15188 4.29038 3.20358 3.22639 3.06334 4.10788 3.47324 3.86421 3.61618 3.47946 2.67390 1.00625 2.88730 5.49222 4.28053 68 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 61 2.89484 4.63395 3.51346 3.36817 4.35306 3.31558 4.43642 3.92611 3.43456 3.54133 4.59617 3.66397 0.65427 3.82016 3.66760 3.06578 3.34480 3.55944 5.51022 4.47541 69 P - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 62 2.83547 5.32344 1.90710 1.42799 4.63051 3.24198 3.71244 4.09996 2.65068 3.63347 4.46321 2.71732 3.81726 2.86723 3.20067 2.75440 2.81778 3.69487 5.81218 4.35094 70 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 63 2.79923 4.56350 3.49435 3.40744 4.54632 0.58454 4.52062 4.17205 3.60289 3.81287 4.79002 3.65874 3.95796 3.91884 3.82676 2.97427 3.28861 3.68020 5.61312 4.65200 71 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 64 2.69344 5.03834 2.59685 1.78499 4.35492 3.31996 3.63904 3.79867 2.33359 3.34661 4.15382 2.64678 2.71516 2.78054 2.89199 2.67010 2.77928 3.42501 5.53498 4.15652 72 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 65 2.70271 4.40317 3.56325 3.00957 3.45446 3.68235 3.94694 2.18180 2.88182 2.21283 3.37093 3.41883 4.05792 2.33611 3.21378 2.95204 2.94041 2.01647 5.02429 3.78732 73 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 66 3.04481 5.17464 2.53544 0.88540 4.53437 3.34332 3.94029 4.00914 2.83416 3.60986 4.58016 2.99593 3.95313 3.15433 3.25317 3.01711 3.35013 3.68253 5.68627 4.40959 74 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 67 3.05681 4.44153 4.54138 3.99838 1.97987 4.22221 4.40129 2.17878 3.87522 1.45215 3.02589 4.20160 4.50632 4.03401 4.02978 3.55251 3.29207 1.80812 4.80289 3.46847 75 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 68 2.82984 5.35567 1.99168 1.57663 4.64578 3.25717 3.68509 4.14274 2.58330 3.63869 4.45307 2.71724 3.81329 2.22362 3.11653 2.74299 3.09347 3.72626 5.79564 4.33600 76 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 69 2.50977 1.62448 4.23724 3.80750 3.60189 3.40590 4.45756 2.35254 3.63764 2.45765 3.57920 3.82230 4.04603 3.92585 3.81907 2.84633 2.91668 1.82275 5.24689 4.01880 77 c - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 70 2.77571 5.11398 2.10801 2.05696 4.45701 3.25620 3.72899 3.91339 2.64389 3.48166 4.32027 2.78446 1.86353 2.89484 3.15510 2.73789 3.05806 3.53410 5.67671 4.27030 78 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 71 2.91274 5.42662 1.24765 1.93231 4.73792 3.20738 3.76458 4.24169 2.78531 3.76893 4.62568 2.68636 3.83308 2.93581 3.37349 2.60161 3.20907 3.82383 5.94007 4.44265 79 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 72 2.93000 5.34144 1.08347 2.15883 4.66482 3.19912 3.82811 4.25255 2.88821 3.80850 4.69751 2.51974 3.85217 3.02158 3.46889 2.84580 3.25390 3.83179 5.90365 4.41772 80 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 73 2.89101 4.40561 4.26922 3.93641 3.62800 3.83108 4.72052 2.04974 3.80577 2.29743 3.57810 4.10920 4.38636 4.15841 4.00806 3.34183 3.25039 0.90272 5.42983 4.16757 81 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 74 3.40066 4.84720 3.99369 3.74344 2.30278 3.95279 3.67128 3.39553 3.59798 2.82228 4.05988 3.85394 4.42456 3.87882 3.75994 3.52665 3.68805 3.27113 3.95029 0.80817 82 y - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 75 3.08173 4.41570 4.73343 4.24332 3.51344 4.38931 4.96241 1.16063 4.11994 2.00857 3.32756 4.46929 4.71466 4.39012 4.32070 3.78014 3.35186 1.39369 5.48545 4.28088 83 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 76 3.27378 4.70553 4.35708 3.99825 3.17780 4.11433 4.62122 2.38848 3.76496 0.75643 3.16963 4.26355 4.53226 4.10824 3.92358 3.69863 3.56359 2.45281 5.09417 3.84135 84 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 77 3.10426 5.24570 0.77891 2.40498 4.63731 3.29196 4.02650 4.24977 3.13093 3.83985 4.82107 2.96628 3.95224 3.26642 3.66070 3.05541 3.44536 3.87811 5.78539 4.49402 85 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 78 2.10165 4.63153 3.04360 2.53313 3.37849 3.42468 3.14974 3.24484 2.48640 2.87927 3.73924 3.02051 3.83549 2.34761 2.89722 2.67591 2.83487 2.96227 5.11406 3.77860 86 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 79 0.87297 4.24657 3.57075 3.36786 4.15839 3.06811 4.37727 3.29971 3.38685 3.17640 4.19749 3.49040 3.81731 3.71861 3.62959 2.59634 2.88098 2.93600 5.57511 4.38724 87 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 80 3.04481 5.17464 2.53544 0.88540 4.53437 3.34332 3.94029 4.00914 2.83416 3.60986 4.58016 2.99593 3.95313 3.15433 3.25317 3.01711 3.35013 3.68253 5.68627 4.40959 88 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 81 3.04481 5.17464 2.53544 0.88540 4.53437 3.34332 3.94029 4.00914 2.83416 3.60986 4.58016 2.99593 3.95313 3.15433 3.25317 3.01711 3.35013 3.68253 5.68627 4.40959 89 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 82 2.02804 4.79412 2.56696 2.04470 4.09359 3.33689 3.67081 3.44631 2.51465 3.10781 3.94410 2.90500 3.80252 2.83547 2.98166 2.64658 2.87169 2.76307 5.37415 4.03168 90 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 83 2.79923 4.56350 3.49435 3.40744 4.54632 0.58454 4.52062 4.17205 3.60289 3.81287 4.79002 3.65874 3.95796 3.91884 3.82676 2.97427 3.28861 3.68020 5.61312 4.65200 91 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 84 2.73428 4.33692 3.73213 3.19478 3.16177 3.72868 2.92126 1.73180 3.00305 2.10225 3.32627 3.53324 4.10443 3.37488 3.27326 3.02489 2.97120 2.37844 4.75364 3.40581 92 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 85 2.98626 5.46880 1.08491 1.97249 4.77077 3.21550 3.81546 4.28421 2.87189 3.82944 4.72170 2.71026 3.86087 3.00007 3.46540 2.87647 3.29141 3.87860 5.96770 4.48798 93 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 86 3.27378 4.70553 4.35708 3.99825 3.17780 4.11433 4.62122 2.38848 3.76496 0.75643 3.16963 4.26355 4.53226 4.10824 3.92358 3.69863 3.56359 2.45281 5.09417 3.84135 94 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 87 2.89484 4.63395 3.51346 3.36817 4.35306 3.31558 4.43642 3.92611 3.43456 3.54133 4.59617 3.66397 0.65427 3.82016 3.66760 3.06578 3.34480 3.55944 5.51022 4.47541 95 P - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 88 3.48726 4.82741 4.35628 4.01269 1.82549 4.23514 3.48811 3.25093 3.87322 2.62544 3.87831 3.93991 4.57991 3.96204 3.99151 3.61127 3.72377 3.16284 3.67256 0.95290 96 y - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 89 2.36871 4.29005 3.29968 3.12112 4.18153 3.01810 4.22768 3.71868 3.20194 3.43114 4.34903 3.32859 3.76571 3.54324 3.48419 0.94365 2.85682 3.23083 5.54583 4.26583 97 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 90 2.70964 0.75093 4.25205 4.01610 3.98428 3.30982 4.64026 3.14621 3.84384 3.05665 4.18165 3.97525 4.02496 4.18572 3.94943 2.98138 3.18527 2.88356 5.37752 4.27103 98 c - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 91 3.12574 4.95602 3.62729 3.11760 4.33719 3.59265 3.90370 3.88680 2.28467 3.38377 4.38192 3.46899 4.09078 3.11945 0.82993 3.20529 3.38498 3.60641 5.37824 4.24257 99 r - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 92 0.87297 4.24657 3.57075 3.36786 4.15839 3.06811 4.37727 3.29971 3.38685 3.17640 4.19749 3.49040 3.81731 3.71861 3.62959 2.59634 2.88098 2.93600 5.57511 4.38724 100 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 93 2.79923 4.56350 3.49435 3.40744 4.54632 0.58454 4.52062 4.17205 3.60289 3.81287 4.79002 3.65874 3.95796 3.91884 3.82676 2.97427 3.28861 3.68020 5.61312 4.65200 101 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 94 2.36871 4.29005 3.29968 3.12112 4.18153 3.01810 4.22768 3.71868 3.20194 3.43114 4.34903 3.32859 3.76571 3.54324 3.48419 0.94365 2.85682 3.23083 5.54583 4.26583 102 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 95 2.70964 0.75093 4.25205 4.01610 3.98428 3.30982 4.64026 3.14621 3.84384 3.05665 4.18165 3.97525 4.02496 4.18572 3.94943 2.98138 3.18527 2.88356 5.37752 4.27103 103 c - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 96 2.36871 4.29005 3.29968 3.12112 4.18153 3.01810 4.22768 3.71868 3.20194 3.43114 4.34903 3.32859 3.76571 3.54324 3.48419 0.94365 2.85682 3.23083 5.54583 4.26583 104 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 97 2.36871 4.29005 3.29968 3.12112 4.18153 3.01810 4.22768 3.71868 3.20194 3.43114 4.34903 3.32859 3.76571 3.54324 3.48419 0.94365 2.85682 3.23083 5.54583 4.26583 105 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 98 2.70964 0.75093 4.25205 4.01610 3.98428 3.30982 4.64026 3.14621 3.84384 3.05665 4.18165 3.97525 4.02496 4.18572 3.94943 2.98138 3.18527 2.88356 5.37752 4.27103 106 c - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 99 0.87297 4.24657 3.57075 3.36786 4.15839 3.06811 4.37727 3.29971 3.38685 3.17640 4.19749 3.49040 3.81731 3.71861 3.62959 2.59634 2.88098 2.93600 5.57511 4.38724 107 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 100 2.79923 4.56350 3.49435 3.40744 4.54632 0.58454 4.52062 4.17205 3.60289 3.81287 4.79002 3.65874 3.95796 3.91884 3.82676 2.97427 3.28861 3.68020 5.61312 4.65200 108 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 101 3.06946 5.03551 3.25229 2.85531 4.44585 3.54670 3.82012 3.88188 0.90373 3.42461 4.38128 3.27486 4.04036 3.00629 2.45564 3.10509 3.31538 3.58407 5.45821 4.28639 109 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 102 3.06247 4.41039 4.65086 4.13598 3.48324 4.35915 4.85935 1.65561 4.00771 1.89605 3.31161 4.38665 4.67296 4.28428 4.22305 3.72759 3.32396 1.08186 5.42132 4.21018 110 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 103 2.33323 4.28075 3.53672 3.04537 3.62455 3.45748 3.98551 2.58410 2.72399 2.59228 3.55231 3.38781 3.95328 3.30102 3.25844 2.79290 2.46624 1.66085 5.10597 3.87716 111 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 104 2.09904 4.31904 3.13967 2.79512 4.23584 2.43802 3.97520 3.66080 2.88605 3.30435 4.12032 2.79615 3.70254 3.18983 3.27753 1.61859 2.49732 3.17574 5.54095 4.27688 112 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 105 2.79923 4.56350 3.49435 3.40744 4.54632 0.58454 4.52062 4.17205 3.60289 3.81287 4.79002 3.65874 3.95796 3.91884 3.82676 2.97427 3.28861 3.68020 5.61312 4.65200 113 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 106 2.34210 4.57052 2.98887 2.43186 3.63497 3.31233 3.71920 3.32573 2.57569 2.97882 3.82112 2.81207 3.79423 2.91349 3.00476 1.86229 2.69145 3.00524 5.25570 3.95436 114 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 107 3.05964 4.41092 4.64145 4.12759 3.48238 4.35054 4.85240 1.66963 3.99735 1.89738 3.31309 4.37857 4.66775 4.27653 4.21363 3.71953 3.32208 1.07763 5.41853 4.20516 115 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 108 2.91005 5.38045 1.25818 2.12941 4.69830 3.20228 3.78776 4.26304 2.81947 3.79137 4.65619 2.14323 3.83796 2.96707 3.40279 2.81725 3.21882 3.83565 5.91563 4.42054 116 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 109 2.96665 4.95377 2.97494 2.73211 4.13599 3.43683 3.89106 3.78353 2.54586 3.27542 4.30113 3.19246 3.99230 1.05904 2.82765 3.01035 3.26391 3.50694 5.38986 4.09082 117 q - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 110 2.64618 4.90499 2.31134 2.18942 4.30332 3.26131 3.70172 3.73572 2.57300 3.32434 4.14511 2.84177 3.78986 2.86174 3.06104 1.76618 2.63178 3.35922 5.54260 4.16860 118 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 111 3.10426 5.24570 0.77891 2.40498 4.63731 3.29196 4.02650 4.24977 3.13093 3.83985 4.82107 2.96628 3.95224 3.26642 3.66070 3.05541 3.44536 3.87811 5.78539 4.49402 119 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 112 2.73269 4.96873 2.61141 2.26957 4.35491 2.17303 3.70728 3.80016 2.46897 3.36392 4.20366 2.88233 3.83451 1.94009 2.87446 2.73151 3.00866 3.43365 5.54626 4.19876 120 q - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 113 2.56630 4.67539 2.76483 2.50324 4.25470 3.20379 3.80042 3.71196 2.47872 3.32135 4.15966 2.47516 3.79205 2.98884 3.00841 1.53662 2.90903 3.30833 5.51362 4.18451 121 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 114 3.45422 4.77029 4.46140 4.11213 1.01250 4.26302 3.55945 3.07075 3.96969 2.40922 3.69615 4.01237 4.59409 4.02617 4.05737 3.63979 3.68916 3.02613 3.73517 1.83750 122 f - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 115 3.27378 4.70553 4.35708 3.99825 3.17780 4.11433 4.62122 2.38848 3.76496 0.75643 3.16963 4.26355 4.53226 4.10824 3.92358 3.69863 3.56359 2.45281 5.09417 3.84135 123 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 116 2.92493 5.35887 1.12201 2.14550 4.68054 3.19834 3.81470 4.26138 2.86788 3.80711 4.68829 2.43062 3.84716 3.00361 3.45124 2.83676 3.24430 3.83759 5.91360 4.42201 124 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02824 3.97705 4.69940 0.61958 0.77255 0.48576 0.95510
+ 117 2.99103 5.43832 1.04731 2.03422 4.75036 3.21916 3.83186 4.26509 2.89245 3.82288 4.72422 2.72815 3.86743 3.02108 3.48036 2.88767 3.30065 3.86474 5.95049 4.48470 125 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.05161 3.97705 3.45590 0.61958 0.77255 0.48576 0.95510
+ 118 2.86997 5.43069 1.57180 1.74614 4.72729 2.80306 3.71453 4.23943 2.69618 3.73332 4.56237 2.43722 3.80910 2.87126 3.27991 2.76596 3.14983 3.81040 5.89719 4.40314 126 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 119 2.94701 4.93449 2.95833 2.71460 4.11381 3.42085 3.87354 3.75736 2.52981 3.25157 4.27740 3.17495 3.97565 1.09531 2.81227 2.99143 3.24405 3.48203 5.37148 4.07074 127 q - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 120 2.77849 4.28259 3.99549 3.02221 3.34513 3.89873 4.21017 1.60238 3.32583 1.96055 3.04166 3.76188 4.24121 3.61775 3.59603 3.18793 3.01465 1.89778 5.01613 3.81900 128 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 121 2.05663 4.99383 2.42035 1.95337 4.30142 3.11016 3.64379 3.74448 2.38547 3.30891 4.11909 2.80952 3.78509 2.79112 2.97996 2.54099 2.92358 3.37653 5.51637 4.13250 129 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 122 2.37074 5.20065 2.03752 1.62561 4.52764 2.94012 3.68254 3.99698 2.59389 3.53203 4.34713 2.73405 3.79399 2.83254 3.13133 2.70217 3.03318 3.59496 5.71621 4.27884 130 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 123 2.76891 4.53595 3.45942 3.36936 4.50963 0.61326 4.48439 4.12940 3.56175 3.77320 4.74981 3.62373 3.92970 3.87945 3.78857 2.94321 3.25651 3.64192 5.58291 4.61439 131 G - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 124 3.45280 4.72560 4.55948 4.18538 1.45983 4.27876 3.45556 3.19175 4.01502 2.56322 3.77632 3.99268 4.58568 4.02082 4.06587 3.62371 3.67122 3.09770 1.76510 1.80304 132 f - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 125 2.87283 4.39315 4.23821 3.90420 3.61058 3.80809 4.69198 2.04849 3.77322 2.28363 3.56364 4.08078 4.36427 4.12727 3.97777 3.31702 3.23254 0.92773 5.40873 4.14528 133 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 126 3.24760 4.68579 4.32075 3.96132 3.16793 4.08580 4.59138 2.37683 3.72825 0.78064 3.16594 4.22883 4.50730 4.07699 3.89079 3.66669 3.53825 2.43535 5.07658 3.81868 134 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 127 2.45786 4.30296 3.50186 3.25812 4.04222 3.13941 4.26905 3.17937 3.20271 3.03994 4.08552 3.45408 3.84975 3.59352 3.45722 2.66008 1.04037 2.86556 5.47283 4.25897 135 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 128 2.68154 0.78852 4.21932 3.97783 3.95068 3.28696 4.60693 3.10838 3.80528 3.02007 4.14415 3.94300 4.00035 4.14805 3.91507 2.95331 3.15521 2.84739 5.34926 4.23772 136 c - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 129 2.02617 4.29048 3.42265 2.94627 3.54036 3.40652 3.31257 2.77872 2.86355 2.59741 3.53948 3.30371 3.90044 3.21666 3.18816 2.73904 2.82169 1.86270 5.00831 3.74432 137 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 130 0.90195 4.23400 3.54659 3.34205 4.13472 3.05626 4.35430 3.27256 3.36043 3.15035 4.17350 3.47069 3.80326 3.69417 3.60509 2.58374 2.86679 2.91280 5.55371 4.36315 138 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 131 3.44381 4.80306 4.30117 3.95207 1.85364 4.19548 3.48537 3.22033 3.81418 2.60484 3.85318 3.90681 4.54641 3.92239 3.94488 3.57229 3.68268 3.12961 3.68006 0.97942 139 y - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 132 2.86235 4.60578 3.47842 3.32948 4.31715 3.28867 4.39999 3.88386 3.39382 3.50174 4.55528 3.62780 0.68858 3.78012 3.62986 3.03247 3.31042 3.51987 5.48103 4.43903 140 P - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 133 2.60256 4.60991 3.08123 2.59418 3.90705 3.39886 3.69738 3.25085 2.27951 2.91739 3.78849 3.05676 3.84470 2.63540 2.79735 2.69573 1.94572 2.76699 5.21418 3.93668 141 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 134 2.16968 3.47307 3.59233 3.22260 4.15866 2.47411 4.19438 3.56363 3.18625 3.27458 4.10858 3.32406 3.66022 3.48496 3.48055 1.23700 2.65371 3.05043 5.52336 4.31592 142 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 135 3.07859 5.21813 0.80740 2.38838 4.60638 3.27362 4.00471 4.21341 3.10456 3.80732 4.78755 2.94873 3.93224 3.24424 3.63163 3.03196 3.41903 3.84400 5.75900 4.46621 143 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 136 2.87283 4.39315 4.23821 3.90420 3.61058 3.80809 4.69198 2.04849 3.77322 2.28363 3.56364 4.08078 4.36427 4.12727 3.97777 3.31702 3.23254 0.92773 5.40873 4.14528 144 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 137 2.50102 4.23694 3.76525 3.33965 3.72246 3.37067 4.24809 2.46042 3.23911 2.55924 3.64161 3.56053 3.97799 3.58142 3.52035 2.77764 1.69802 1.75863 5.30971 4.08018 145 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 138 3.09498 4.49149 4.45102 4.07022 3.43002 4.15408 4.78347 0.98199 3.89992 1.99977 3.35310 4.30411 4.57779 4.24002 4.08717 3.65761 3.39284 1.85079 5.33749 4.08258 146 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 139 3.02382 5.15051 2.52384 0.91441 4.50717 3.32764 3.92196 3.97736 2.81286 3.58149 4.55225 2.98104 3.93620 3.13613 3.22992 2.99812 3.32879 3.65289 5.66334 4.38601 147 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 140 2.45786 4.30296 3.50186 3.25812 4.04222 3.13941 4.26905 3.17937 3.20271 3.03994 4.08552 3.45408 3.84975 3.59352 3.45722 2.66008 1.04037 2.86556 5.47283 4.25897 148 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 141 3.08695 4.88934 3.20791 2.97643 3.34377 3.51816 0.98092 3.80251 2.81733 3.28606 4.33566 3.38232 4.07539 3.34383 3.07797 3.15699 3.39324 3.53609 4.80769 3.29239 149 h - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 142 2.99214 5.06805 3.26268 2.74531 4.47846 3.57206 3.65342 3.86981 1.12103 3.36156 4.25702 3.16311 3.99796 2.80635 2.11223 3.00404 3.19554 3.55761 5.42835 4.23089 150 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 143 3.02382 5.15051 2.52384 0.91441 4.50717 3.32764 3.92196 3.97736 2.81286 3.58149 4.55225 2.98104 3.93620 3.13613 3.22992 2.99812 3.32879 3.65289 5.66334 4.38601 151 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 144 2.49167 5.21869 2.13891 1.38935 4.54510 3.23855 3.71342 3.98470 2.64038 3.55288 4.39217 2.73628 3.81159 2.87379 3.17028 2.74234 3.08340 3.59770 5.74876 4.31122 152 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 145 2.67924 5.36825 1.81597 1.42545 4.67130 3.22067 3.71949 4.14895 2.68617 3.67868 4.51726 2.69278 3.81366 2.87890 3.25116 2.76699 3.13943 3.73938 5.85528 4.37934 153 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 146 3.24708 4.60677 4.69416 4.13988 3.08947 4.47063 4.76500 1.92492 3.96672 0.95356 2.71915 4.43331 4.67883 4.15873 4.13317 3.81764 3.47493 2.15974 5.15578 4.04247 154 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02889 3.95434 4.67668 0.61958 0.77255 0.50828 0.92013
+ 147 2.69781 4.29649 3.84369 3.29786 3.44437 3.73086 4.15124 2.24231 3.19336 2.10104 3.11890 3.63278 4.14347 3.51043 3.49251 3.03876 2.03846 1.78833 5.07714 3.86271 155 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.18495 3.95434 1.89921 0.61958 0.77255 0.50828 0.92013
+ 148 1.44115 4.10304 3.22225 2.99375 4.15355 2.08176 4.10711 3.47540 3.09081 3.24183 4.11431 3.18864 3.61518 3.39097 3.39593 2.35434 2.65737 2.99565 5.50492 4.29375 156 a - - -
+ 2.68608 4.42226 2.77520 2.73124 3.46354 2.40513 3.72495 3.29355 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37887 2.77520 2.98519 4.58477 3.61504
+ 0.08120 2.55114 * 0.46726 0.98542 0.00000 *
+//
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html#Jalview.2.10.3b1"/>
+ <mapID target="release" url="html/releases.html#Jalview.2.10.4"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
+ <mapID target="alwHmmer" url="html/menus/alwhmmer.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
<mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
<mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<tocitem text="Colour Menu" target="alwColour" />
<tocitem text="Calculate Menu" target="alwCalc" />
<tocitem text="Web Service Menu" target="wsMenu" />
+ <tocitem text="HMMER Menu" target="alwHmmer" />
<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
<tocitem text="Popup Menu" target="popMenu" />
</tocitem>
sequence alignments and EPS files.
</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of
- sequence alignments and EPS files.
+ Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+ </li>
+ <li>The <a href="#hmmer"><strong>"HMMER"</strong>
+ Preferences</a> tab allows you to configure locally installed HMMER tools.
</li>
<li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS
<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p> </p>
- <p> </p>
+ <p>
+ <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
+ </p>
+ <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+ then you should specify on this screen the location of the installation (the path to the folder
+ containing binary executable programs). Double-click in the input field to open a file browser.</p>
+ <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+ enabled in the Alignment window.</p>
</body>
</html>
or <strong>"View→Nucleotide"</strong> (in the protein panel)
allows you to show or hide one or other of the linked alignment
panels.</li>
- <li>Panel heights are adjusted dragging the divider between
+ <li>Panel heights are adjusted by dragging the divider between
them using the mouse</li>
<li><a href="../menus/alwview.html"><strong>"View→New
View / Expand Views / Gather Views"</strong></a> behave as for a normal
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+</head>
+<body>
+<p>
+ <strong>HMMER Menu</strong>
+</p>
+<p>This menu is available if hmmbuild tools have been installed and configured in the
+<a href="../features/preferences.html#hmmer">HMMER Preferences</a> panel.
+ <br><br>
+
+ <strong>hmmbuild</strong>
+ <br><br>Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups.
+ <br><br>The consensus sequence for the computed profile is inserted as the first sequence of
+ the alignment (or group) for which hmmbuild is run.
+ <br>Jalview also computes and displays an annotation below the alignment, showing
+ the information content of each column.
+ <br>This is calculated as the sum over residue symbols of
+ <pre>
+ match emission probability * log(match emission probability / background frequency) / log(2)
+ </pre>
+ where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats)
+ <ul>
+ <li>Edit settings and run...
+ <br><br>Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both
+ (default is the alignment).
+ <br>Optionally enter a name to give the HMM profile consensus sequence
+ (default is "Alignment" or group name, with "_HMM" appended).
+ <br>Use Reference Annotation: select this option if your alignment has an RF reference annotation,
+ and you wish to constrain the HMM profile to it (hmmbuild option '--hand').
+ <br><br></li>
+ <li>hmmbuild with default settings
+ <br><br>Runs hmmbuild for the whole alignment.</li>
+ </ul>
+
+ <strong>hmmalign</strong> and <strong>hmmsearch</strong> require an HMM consensus sequence to be selected first.
+ <br><em>To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'.
+ The alignment will be with respect to the HMM profile for the consensus sequence.</em>
+ <br><br>
+ <strong>hmmalign</strong>
+ <br><br>Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile.
+ <ul>
+ <li>Edit settings and run...
+ <br><br>Choose whether to 'trim non-matching termini' - hmmalign option '--trim'.
+ <br><br></li>
+ <li>hmmalign with default settings</li>
+ </ul>
+ <strong>hmmsearch</strong>
+ <br><br>Run hmmsearch to use an HMM profile as input to search a sequence database.
+ <ul>
+ <li>Edit settings and run...
+ <ul>
+ <li>tbc: choose database</li>
+ <li>tbc: automatically align</li>
+ <li>tbc: return accessions</li>
+ <li>tbc: number of results</li>
+ <li>tbc: sequence eValue cutoff</li>
+ <li>tbc: domains eValue cutoff</li>
+ </ul>
+ </li>
+ <br><li>hmmsearch with default settings</li>
+ <br><li>Add database
+ <br>Browse to select a local sequence data file to be searched</li>
+ </ul>
+<br>
+</body>
+</html>
<tr>
<td width="60" nowrap>
<div align="center">
+ <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
+ <li>
+ <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services
+ </li>
+ <li>
+ <!-- JAL-2759 -->Improved performance for large alignments and lots of hidden columns
+ </li>
+ </ul>
+ </div>
+ </td>
+ <td><div align="left">
+ <ul>
+ <li>
+ <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
+ </li>
+ <li>
+ <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
+ </li>
+ <li><!-- JAL-2930 -->Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
+ <li><!-- JAL-2924 -->Tooltip shouldn't be displayed for empty columns in annotation row</li>
+ <li><!-- JAL-2913 -->Preferences panel's ID Width control is honored in interactive and batch mode</li>
+ </ul><em>Applet</em><ul>
+ <li><!-- JAL-2926 -->Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
+
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
<strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
</div>
</td>
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.3b1 ?</strong>
+ <strong>What's new in Jalview 2.10.4 ?</strong>
</p>
<p>
- This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures.
- The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
- Release Notes</a>. In addition, Jalview 2.10.3 provides:
+ This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements.
+ The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>. In addition, Jalview 2.10.4 provides:
</p>
<ul>
- <li>Faster and more responsive UI when importing and working
- with wide alignments and handling hundreds and thousands of
- sequence features</li>
- <li>Improved usability with <a
- href="features/pdbsequencefetcher.html">PDB</a> and <a
- href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
- Search dialog, and new tab for retrieval of sequences for lists of
- IDs.
- </li>
- <li>Short names assigned to sequences retrieved from UniProt</li>
- <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
+ <li></li>
</ul>
<p>
<strong><a name="experimental">Experimental Features</a></strong>
action.show_html_source = Show HTML Source
action.print = Print...
action.web_service = Web Service
+action.hmmer = HMMER
action.cancel_job = Cancel Job
action.start_job = Start Job
action.revert = Revert
label.colourScheme_nucleotide = Nucleotide
label.colourScheme_t-coffee_scores = T-Coffee Scores
label.colourScheme_rna_helices = By RNA Helices
+label.colourScheme_hmmer-uniprot = HMMER profile v global background
+label.colourScheme_hmmer-alignment = HMMER profile v alignment background
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
status.searching_for_pdb_structures = Searching for PDB Structures
status.opening_file_for = opening file for
status.colouring_chimera = Colouring Chimera
+status.running_hmmbuild = Building Hidden Markov Model
+status.running_hmmalign = Creating alignment with Hidden Markov Model
+status.running_hmmsearch = Searching for matching sequences
label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
label.font_too_small = Font size is too small
label.error_loading_file_params = Error loading file {0}
label.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+label.hmmalign = hmmalign
+label.hmmbuild = hmmbuild
+label.hmmbuild_group = Build HMM from Selected Group
+label.group_hmmbuild = Build HMM from Group
+label.hmmsearch = hmmsearch
+label.hmmer_location = HMMER Binaries Installation Location
+warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
+label.ignore_below_background_frequency = Ignore Below Background Frequency
+label.information_description = Information content, measured in bits
+warn.no_selected_hmm = Please select a hidden Markov model sequence.
+label.select_hmm = Select HMM
+warn.no_sequence_data = No sequence data found.
+warn.empty_grp_or_alignment = An empty group or alignment was found.
+label.no_sequences_found = No matching sequences, or an error occurred.
+label.hmmer = HMMER
+label.trim_termini = Trim Non-Matching Termini
+label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
+label.no_of_sequences = Sequences Returned
+label.freq_alignment = Use Alignment Background Frequencies
+label.freq_uniprot = Use Uniprot Background Frequencies
+label.hmmalign_label = hmmalign Options
+label.hmmsearch_label = hmmsearch Options
+label.hmmbuild_not_found = The hmmbuild binary was not found
+label.hmmalign_not_found = The hmmalign binary was not found
+label.hmmsearch_not_found = The hmmsearch binary was not found
+warn.hmm_command_failed = hmm command not found
+label.invalid_folder = Invalid Folder
+label.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed).
+label.hmmer_installed = HMMER installed
+label.hmmer_no_sequences_found = No sequences found
+label.number_of_results = Number of Results to Return
+label.auto_align_seqs = Automatically Align Fetched Sequences
+label.use_accessions = Return Accessions
+label.seq_e_value = Sequence E-value Cutoff
+label.seq_score = Sequence Score Threshold
+label.dom_e_value = Domain E-value Cutoff
+label.dom_score = Domain Score Threshold
+label.number_of_results_desc = The maximum number of results that hmmsearch will return
+label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequences name
+label.seq_e_value_desc = The E-value cutoff for returned sequences
+label.seq_score_desc = The score threshold for returned sequences
+label.dom_e_value_desc = The E-value cutoff for returned domains
+label.dom_score_desc = The score threshold for returned domains
+label.not_enough_sequences = There are not enough sequences to run {0}
+label.add_database = Add Database
+label.this_alignment = This alignment
+warn.file_not_exists = File does not exist
+warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
+label.database_for_hmmsearch = The database hmmsearch will search through
+label.use_reference = Use Reference Annotation
+label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation
+label.hmm_name = HMM Name
+label.hmm_name_desc = The name given to the HMM.
+warn.no_reference_annotation = No reference annotation found.
+label.hmmbuild_for = Build HMM for
+label.hmmbuild_for_desc = Build an HMM for the selected sequence groups.
+label.alignment = Alignment
+label.groups_and_alignment = All groups and alignment
+label.groups = All groups
+label.selected_group = Selected group
+label.use_info_for_height = Use Information Content as Letter Height
}
/**
+ * Annotate the residues with their corresponding positions in s1 using the
+ * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+ * structure.
+ *
+ * @param as
+ * @param s1
+ */
+ public void makeExactMapping(StructureMapping mapping, SequenceI s1)
+ {
+ // first clear out any old alignmentMapping values:
+ for (Atom atom : atoms)
+ {
+ atom.alignmentMapping = -1;
+ }
+ SequenceI ds = s1;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ int pdboffset = 0;
+ for (Residue res : residues)
+ {
+ // res.number isn't set correctly for discontinuous/mismapped residues
+ int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
+ char strchar = sequence.getCharAt(pdboffset++);
+ if (seqpos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ continue;
+ }
+ char seqchar = ds.getCharAt(seqpos - ds.getStart());
+
+ boolean sameResidue = Comparison.isSameResidue(
+ seqchar, strchar, false);
+ if (sameResidue)
+ {
+ for (Atom atom : res.atoms)
+ {
+ atom.alignmentMapping = seqpos - 1;
+ }
+ }
+ }
+ }
+
+ /**
* Copies over the RESNUM seqfeatures from the internal chain sequence to the
* mapped sequence
*
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
+ if (sqmpping == null)
+ {
+ // SIFTS mappings are recorded in the StructureMapping object...
+
+ sqmpping = mapping.getSeqToPdbMapping();
+ }
if (sq != null)
{
while (dsq.getDatasetSequence() != null)
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
import jalview.datamodel.Profiles;
import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
+import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MappingUtils;
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
*
- * @author $author$
- * @version $Revision$
*/
public class AAFrequency
{
- public static final String PROFILE = "P";
-
- /*
- * Quick look-up of String value of char 'A' to 'Z'
- */
- private static final String[] CHARS = new String['Z' - 'A' + 1];
+ private static final double LOG2 = Math.log(2);
- static
- {
- for (char c = 'A'; c <= 'Z'; c++)
- {
- CHARS[c - 'A'] = String.valueOf(c);
- }
- }
+ public static final String PROFILE = "P";
public static final ProfilesI calculate(List<SequenceI> list, int start,
int end)
}
/**
+ * Returns the full set of profiles for a hidden Markov model. The underlying
+ * data is the raw probabilities of a residue being emitted at each node,
+ * however the profiles returned by this function contain the percentage
+ * chance of a residue emission.
+ *
+ * @param hmm
+ * @param width
+ * The width of the Profile array (Profiles) to be returned.
+ * @param start
+ * The alignment column on which the first profile is based.
+ * @param end
+ * The alignment column on which the last profile is based.
+ * @param removeBelowBackground
+ * if true, symbols with a match emission probability less than
+ * background frequency are ignored
+ * @return
+ */
+ public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
+ int width, int start, int end, boolean removeBelowBackground,
+ boolean infoLetterHeight)
+ {
+ ProfileI[] result = new ProfileI[width];
+ char[] symbols = hmm.getSymbols().toCharArray();
+ int symbolCount = symbols.length;
+ for (int column = start; column < end; column++)
+ {
+ ResidueCount counts = new ResidueCount();
+ for (char symbol : symbols)
+ {
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground, infoLetterHeight);
+ counts.put(symbol, value);
+ }
+ int maxCount = counts.getModalCount();
+ String maxResidue = counts.getResiduesForCount(maxCount);
+ int gapCount = counts.getGapCount();
+ ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
+ maxResidue);
+ profile.setCounts(counts);
+
+ result[column] = profile;
+ }
+ return new Profiles(result);
+ }
+
+ /**
* Make an estimate of the profile size we are going to compute i.e. how many
* different characters may be present in it. Overestimating has a cost of
* using more memory than necessary. Underestimating has a cost of needing to
}
/**
- * Derive the gap count annotation row.
+ * Derive the information annotations to be added to the alignment for
+ * display. This does not recompute the raw data, but may be called on a
+ * change in display options, such as 'ignore below background frequency',
+ * which may in turn result in a change in the derived values.
*
- * @param gaprow
+ * @param information
+ * the annotation row to add annotations to
+ * @param profiles
+ * the source information data
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
+ * @param ignoreGaps
+ * if true, normalise residue percentages
+ * @param showSequenceLogo
+ * if true include all information symbols, else just show modal
+ * residue
+ */
+ public static float completeInformation(AlignmentAnnotation information,
+ ProfilesI profiles, int startCol, int endCol)
+ {
+ // long now = System.currentTimeMillis();
+ if (information == null || information.annotations == null)
+ {
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return 0;
+ }
+
+ float max = 0f;
+ SequenceI hmmSeq = information.sequenceRef;
+
+ int seqLength = hmmSeq.getLength();
+ if (information.annotations.length < seqLength)
+ {
+ return 0;
+ }
+
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+
+ for (int column = startCol; column < endCol; column++)
+ {
+ if (column >= seqLength)
+ {
+ // hmm consensus sequence is shorter than the alignment
+ break;
+ }
+
+ float value = hmm.getInformationContent(column);
+ boolean isNaN = Float.isNaN(value);
+ if (!isNaN)
+ {
+ max = Math.max(max, value);
+ }
+
+ String description = isNaN ? null
+ : String.format("%.4f bits", value);
+ information.annotations[column] = new Annotation(
+ Character.toString(
+ Character.toUpperCase(hmmSeq.getCharAt(column))),
+ description, ' ', value);
+ }
+
+ information.graphMax = max;
+ return max;
+ }
+
+ /**
+ * Derive the occupancy count annotation
+ *
+ * @param occupancy
* the annotation row to add annotations to
* @param profiles
* the source consensus data
* @param endCol
* end column (exclusive)
*/
- public static void completeGapAnnot(AlignmentAnnotation gaprow,
+ public static void completeOccupancyAnnot(AlignmentAnnotation occupancy,
ProfilesI profiles, int startCol, int endCol, long nseq)
{
- if (gaprow == null || gaprow.annotations == null
- || gaprow.annotations.length < endCol)
+ if (occupancy == null || occupancy.annotations == null
+ || occupancy.annotations.length < endCol)
{
/*
* called with a bad alignment annotation row
return;
}
// always set ranges again
- gaprow.graphMax = nseq;
- gaprow.graphMin = 0;
+ occupancy.graphMax = nseq;
+ occupancy.graphMin = 0;
double scale = 0.8 / nseq;
for (int i = startCol; i < endCol; i++)
{
* happens if sequences calculated over were
* shorter than alignment width
*/
- gaprow.annotations[i] = null;
+ occupancy.annotations[i] = null;
return;
}
String description = "" + gapped;
- gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+ occupancy.annotations[i] = new Annotation("", description, '\0',
+ gapped,
jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
(float) scale * gapped));
}
return result;
}
+
/**
* Extract a sorted extract of cDNA codon profile data. The returned array
* contains
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, int[]> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
}
return scale;
}
+
+ /**
+ * Returns the sorted HMM profile for the given column of the alignment. The
+ * returned array contains
+ *
+ * <pre>
+ * [profileType=0, numberOfValues, 100, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value
+ * </pre>
+ *
+ * @param hmm
+ * @param column
+ * @param removeBelowBackground
+ * if true, ignores residues with probability less than their
+ * background frequency
+ * @param infoHeight
+ * if true, uses the log ratio 'information' measure to scale the
+ * value
+ * @return
+ */
+ public static int[] extractHMMProfile(HiddenMarkovModel hmm, int column,
+ boolean removeBelowBackground, boolean infoHeight)
+ {
+ if (hmm == null)
+ {
+ return null;
+ }
+ String alphabet = hmm.getSymbols();
+ int size = alphabet.length();
+ char symbols[] = new char[size];
+ int values[] = new int[size];
+ int totalCount = 0;
+
+ for (int i = 0; i < size; i++)
+ {
+ char symbol = alphabet.charAt(i);
+ symbols[i] = symbol;
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground, infoHeight);
+ values[i] = value;
+ totalCount += value;
+ }
+
+ /*
+ * sort symbols by increasing emission probability
+ */
+ QuickSort.sort(values, symbols);
+
+ int[] profile = new int[3 + size * 2];
+
+ profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ profile[1] = size;
+ profile[2] = 100;
+
+ /*
+ * order symbol/count profile by decreasing emission probability
+ */
+ if (totalCount != 0)
+ {
+ int arrayPos = 3;
+ for (int k = size - 1; k >= 0; k--)
+ {
+ Float percentage;
+ int value = values[k];
+ if (removeBelowBackground)
+ {
+ percentage = ((float) value) / totalCount * 100f;
+ }
+ else
+ {
+ percentage = value / 100f;
+ }
+ int intPercent = Math.round(percentage);
+ profile[arrayPos] = symbols[k];
+ profile[arrayPos + 1] = intPercent;
+ arrayPos += 2;
+ }
+ }
+ return profile;
+ }
+
+ /**
+ * Converts the emission probability of a residue at a column in the alignment
+ * to a 'count', suitable for rendering as an annotation value
+ *
+ * @param hmm
+ * @param column
+ * @param symbol
+ * @param removeBelowBackground
+ * if true, returns 0 for any symbol with a match emission
+ * probability less than the background frequency
+ * @infoHeight if true, uses the log ratio 'information content' to scale the
+ * value
+ * @return
+ */
+ static int getAnalogueCount(HiddenMarkovModel hmm, int column,
+ char symbol, boolean removeBelowBackground, boolean infoHeight)
+ {
+ double value = hmm.getMatchEmissionProbability(column, symbol);
+ double freq = ResidueProperties.backgroundFrequencies
+ .get(hmm.getAlphabetType()).get(symbol);
+ if (value < freq && removeBelowBackground)
+ {
+ return 0;
+ }
+
+ if (infoHeight)
+ {
+ value = value * (Math.log(value / freq) / LOG2);
+ }
+
+ value = value * 10000d;
+ return Math.round((float) value);
+ }
}
* @param seqMappings
* the set of mappings involving dnaSeq
* @param aMapping
- * an initial candidate from seqMappings
+ * a transcript-to-peptide mapping
* @return
*/
static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,
if (mappedFromLength == dnaLength
|| mappedFromLength == dnaLength - CODON_LENGTH)
{
- return seqDss;
+ /*
+ * if sequence has CDS features, this is a transcript with no UTR
+ * - do not take this as the CDS sequence! (JAL-2789)
+ */
+ if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS)
+ .isEmpty())
+ {
+ return seqDss;
+ }
}
/*
{
/*
* found a 3:1 mapping to the protein product which covers
- * the whole dna sequence i.e. is from CDS; finally check it
- * is from the dna start sequence
+ * the whole dna sequence i.e. is from CDS; finally check the CDS
+ * is mapped from the given dna start sequence
*/
SequenceI cdsSeq = map.getFromSeq();
+ // todo this test is weak if seqMappings contains multiple mappings;
+ // we get away with it if transcript:cds relationship is 1:1
List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils
.findMappingsForSequence(cdsSeq, seqMappings);
if (!dnaToCdsMaps.isEmpty())
protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
SequenceI contig, SequenceI proteinProduct, Mapping mapping)
{
+
// gather direct refs from contig congruent with mapping
List<DBRefEntry> direct = new ArrayList<>();
HashSet<String> directSources = new HashSet<>();
+
if (contig.getDBRefs() != null)
{
for (DBRefEntry dbr : contig.getDBRefs())
int mappedDnaLength = MappingUtils.getLength(ranges);
/*
- * if not a whole number of codons, something is wrong,
- * abort mapping
+ * if not a whole number of codons, truncate mapping
*/
- if (mappedDnaLength % CODON_LENGTH > 0)
+ int codonRemainder = mappedDnaLength % CODON_LENGTH;
+ if (codonRemainder > 0)
{
- return null;
+ mappedDnaLength -= codonRemainder;
+ MappingUtils.removeEndPositions(codonRemainder, ranges);
}
int proteinLength = proteinSeq.getLength();
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
public class Dna
* 'final' variables describe the inputs to the translation, which should not
* be modified.
*/
- final private List<SequenceI> selection;
+ private final List<SequenceI> selection;
- final private String[] seqstring;
+ private final String[] seqstring;
- final private int[] contigs;
+ private final Iterator<int[]> contigs;
- final private char gapChar;
+ private final char gapChar;
- final private AlignmentAnnotation[] annotations;
+ private final AlignmentAnnotation[] annotations;
- final private int dnaWidth;
+ private final int dnaWidth;
- final private AlignmentI dataset;
+ private final AlignmentI dataset;
+
+ private ShiftList vismapping;
+
+ private int[] startcontigs;
/*
* Working variables for the translation.
* @param viewport
* @param visibleContigs
*/
- public Dna(AlignViewportI viewport, int[] visibleContigs)
+ public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)
{
this.selection = Arrays.asList(viewport.getSequenceSelection());
this.seqstring = viewport.getViewAsString(true);
this.annotations = viewport.getAlignment().getAlignmentAnnotation();
this.dnaWidth = viewport.getAlignment().getWidth();
this.dataset = viewport.getAlignment().getDataset();
+ initContigs();
+ }
+
+ /**
+ * Initialise contigs used as starting point for translateCodingRegion
+ */
+ private void initContigs()
+ {
+ vismapping = new ShiftList(); // map from viscontigs to seqstring
+ // intervals
+
+ int npos = 0;
+ int[] lastregion = null;
+ ArrayList<Integer> tempcontigs = new ArrayList<>();
+ while (contigs.hasNext())
+ {
+ int[] region = contigs.next();
+ if (lastregion == null)
+ {
+ vismapping.addShift(npos, region[0]);
+ }
+ else
+ {
+ // hidden region
+ vismapping.addShift(npos, region[0] - lastregion[1] + 1);
+ }
+ lastregion = region;
+ tempcontigs.add(region[0]);
+ tempcontigs.add(region[1]);
+ }
+
+ startcontigs = new int[tempcontigs.size()];
+ int i = 0;
+ for (Integer val : tempcontigs)
+ {
+ startcontigs[i] = val;
+ i++;
+ }
+ tempcontigs = null;
}
/**
List<SequenceI> proteinSeqs)
{
List<int[]> skip = new ArrayList<>();
- int skipint[] = null;
- ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
- // intervals
- int vc;
- int[] scontigs = new int[contigs.length];
+ int[] skipint = null;
+
int npos = 0;
- for (vc = 0; vc < contigs.length; vc += 2)
- {
- if (vc == 0)
- {
- vismapping.addShift(npos, contigs[vc]);
- }
- else
- {
- // hidden region
- vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
- }
- scontigs[vc] = contigs[vc];
- scontigs[vc + 1] = contigs[vc + 1];
- }
+ int vc = 0;
+
+ int[] scontigs = new int[startcontigs.length];
+ System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
// allocate a roughly sized buffer for the protein sequence
StringBuilder protein = new StringBuilder(seqstring.length() / 2);
*/
package jalview.analysis;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
/**
* Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
+ * Keys are Name, Start, End, SeqFeatures, PdbId, HMM
*
* @param seq
* SequenceI
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
}
+ if (seq.isHMMConsensusSequence())
+ {
+ sqinfo.put("HMM", seq.getHMM());
+ }
return sqinfo;
}
Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
+ HiddenMarkovModel hmm = (HiddenMarkovModel) sqinfo.get("HMM");
if (oldname == null)
{
namePresent = false;
sq.setDatasetSequence(seqds);
}
+ if (hmm != null)
+ {
+ sq.setHMM(new HiddenMarkovModel(hmm));
+ sq.setIsHMMConsensusSequence(true);
+ }
return namePresent;
}
/**
* Updates the display of calculated annotation values (does not recalculate
- * the values). This allows ßquick redraw of annotations when display settings
- * are changed.
+ * the values). This allows a quick redraw of annotations when display
+ * settings are changed.
*/
void updateAnnotation();
*
* @return
*/
- public ViewportRanges getRanges();
+ ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*
* @return total height of annotation
*/
- public int calcPanelHeight();
+ int calcPanelHeight();
/**
* Answers true if the viewport has at least one column selected
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
ColumnSelection getColumnSelection();
- ProfilesI getSequenceConsensusHash();
+ ProfilesI getConsensusProfiles();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
*
* @return
*/
- AlignmentAnnotation getAlignmentGapAnnotation();
+ AlignmentAnnotation getOccupancyAnnotation();
/**
* get the container for cDNA complement consensus annotation
*
* @param hconsensus
*/
- void setSequenceConsensusHash(ProfilesI hconsensus);
+ void setConsensusProfiles(ProfilesI hconsensus);
/**
* Set the cDNA complement consensus for the viewport
*
* @return a copy of this view's current display settings
*/
- public ViewStyleI getViewStyle();
+ ViewStyleI getViewStyle();
/**
* update the view's display settings with the given style set
*
* @param settingsForView
*/
- public void setViewStyle(ViewStyleI settingsForView);
+ void setViewStyle(ViewStyleI settingsForView);
/**
* Returns a viewport which holds the cDna for this (protein), or vice versa,
*/
void setFollowHighlight(boolean b);
- public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+ void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
* check if current selection group is defined on the view, or is simply a
@Override
void setProteinFontAsCdna(boolean b);
- public abstract TreeModel getCurrentTree();
+ void setHmmProfiles(ProfilesI info);
+
+ ProfilesI getHmmProfiles();
+
+ /**
+ * Registers and starts a worker thread to calculate Information Content
+ * annotation, if it is not already registered
+ *
+ * @param ap
+ */
+ void initInformationWorker(AlignmentViewPanel ap);
+
+ boolean isInfoLetterHeight();
+
+ abstract TreeModel getCurrentTree();
- public abstract void setCurrentTree(TreeModel tree);
+ abstract void setCurrentTree(TreeModel tree);
}
*/
void setJalviewColourScheme(ColourSchemeI colourScheme);
+ /**
+ *
+ * @return true if all background sequence/structure binding threads have
+ * completed for this viewer instance
+ */
+ boolean hasMapping();
+
}
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.initInformationWorker(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
static StringBuffer copiedSequences;
- static Vector<int[]> copiedHiddenColumns;
+ static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector<>(viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : copiedHiddenColumns)
- {
- region[0] = region[0] - hiddenOffset;
- region[1] = region[1] - hiddenOffset;
- }
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ copiedHiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
else
{
{
try
{
-
if (copiedSequences == null)
{
return;
}
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+ "\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ af.viewport.setHiddenColumns(copiedHiddenColumns);
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
*
* This file is part of Jalview.
*
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
private AnnotationColumnChooser annotationColumnSelectionState;
+ java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
if (colour != null)
{
residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(alignment, colour));
+ ColourSchemeProperty.getColourScheme(getAlignment(),
+ colour));
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
}
}
initAutoAnnotation();
-
}
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- private float heightScale = 1, widthScale = 1;
-
/**
* {@inheritDoc}
*/
.getStructureSelectionManager(applet);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
if (av.hasHiddenColumns())
{
AlignmentI al = av.getAlignment();
- start = al.getHiddenColumns().findColumnPosition(ostart);
- end = al.getHiddenColumns().findColumnPosition(end);
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
if (start == end)
{
if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out.println(
- "adjustAnnotationHeight frame size zero NEEDS FIXING");
+ // panel not laid out yet?
+ return;
}
fontChanged();
validateAnnotationDimensions(true);
if (av.hasHiddenColumns())
{
width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
+ .absoluteToVisibleColumn(width);
}
if (x < 0)
{
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.awt.event.MouseMotionListener;
import java.util.Arrays;
import java.util.Collections;
-import java.util.Vector;
public class AnnotationLabels extends Panel
implements ActionListener, MouseListener, MouseMotionListener
{
Image image;
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
+ private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
boolean active = false;
AlignmentPanel ap;
this.ap = ap;
this.av = ap.av;
setLayout(null);
-
- /**
- * this retrieves the adjustable height glyph from resources. we don't use
- * it at the moment. java.net.URL url =
- * getClass().getResource("/images/idwidth.gif"); Image temp = null;
- *
- * if (url != null) { temp =
- * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
- *
- * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
- * mt.waitForID(0); } catch (Exception ex) { }
- *
- * BufferedImage bi = new BufferedImage(temp.getHeight(this),
- * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
- * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
- * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
- */
addMouseListener(this);
addMouseMotionListener(this);
}
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons = av.getConsensusSeq();
+ SequenceGroup group = aa[selectedRow].groupRef;
+ SequenceI cons = group == null ? av.getConsensusSeq()
+ : group.getConsensusSeq();
if (cons != null)
{
copy_annotseqtoclipboard(cons);
@Override
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
setCursor(Cursor.getPredefinedCursor(
resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
int row = getSelectedRow(evt.getY() + scrollOffset);
MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null)
? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus()
+ .isIgnoreGapsConsensus()
: ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
+ "\t" + sq.getSequenceAsString() + "\n");
if (av.hasHiddenColumns())
{
- jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
- av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
}
}
}
g.translate(0, +scrollOffset);
- if (resizePanel)
- {
- // g.setColor(Color.red);
- // g.setPaintMode();
- // g.drawLine(2, 8, 5, 2);
- // g.drawLine(5, 2, 8, 8);
- }
- else if (!dragCancelled && dragEvent != null && aa != null)
+
+ if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
if (av.hasHiddenColumns())
{
column = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(column);
+ .visibleToAbsoluteColumn(column);
}
if (row > -1 && column < aa[row].annotations.length
public class FeatureSettings extends Panel
implements ItemListener, MouseListener, MouseMotionListener,
- ActionListener, AdjustmentListener, FeatureSettingsControllerI
+ AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
add(scrollPane, BorderLayout.CENTER);
}
- Button invert = new Button("Invert Selection");
- invert.addActionListener(this);
+ Button invert = new Button(
+ MessageManager.getString("label.invert_selection"));
+ invert.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSelection();
+ }
+ });
Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
lowerPanel.add(invert);
}
}
- @Override
- public void actionPerformed(ActionEvent evt)
+ protected void invertSelection()
{
for (int i = 0; i < featurePanel.getComponentCount(); i++)
{
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int annotationHeight = 0;
*/
package jalview.appletgui;
+import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.Image;
import java.awt.Panel;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
int oldX = 0;
- Image image;
-
AlignmentPanel ap;
public IdwidthAdjuster(AlignmentPanel ap)
{
setLayout(null);
this.ap = ap;
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
- }
-
+ setBackground(Color.WHITE);
addMouseListener(this);
addMouseMotionListener(this);
}
public void mouseClicked(MouseEvent evt)
{
}
-
- @Override
- public void paint(Graphics g)
- {
- // g.setColor(Color.white);
- // g.fillRect(0, 0, getSize().width, getSize().height);
- // if (active)
- // {
- // if (image != null)
- // {
- // g.drawImage(image, getSize().width - 20, 2, this);
- // }
- // }
- }
-
}
od.getColumns(av.getAlignment()));
mg.translate(0, -od.getSequencesHeight());
}
- System.gc();
if (restart)
{
od = new OverviewDimensionsShowHidden(av.getRanges(),
(av.isShowAnnotation()
- && av.getSequenceConsensusHash() != null));
+ && av.getConsensusProfiles() != null));
oviewCanvas = new OverviewCanvas(od, av);
setLayout(new BorderLayout());
if (!od.isPositionInBox(evt.getX(), evt.getY()))
{
draggingBox = false;
+
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
@Override
public void mouseReleased(MouseEvent evt)
{
+ draggingBox = false;
}
@Override
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
public class ScalePanel extends Panel
if (av.hasHiddenColumns())
{
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
}
else
{
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasManyHiddenColumns())
+ if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
{
item = new MenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
if (!stretchingGroup)
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
res = Math.max(0, res);
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
res = Math.min(res, av.getAlignment().getWidth() - 1);
min = Math.min(res, min);
max = Math.max(res, max);
{
if (hidden.isVisible(sel))
{
- sel = hidden.findColumnPosition(sel);
+ sel = hidden.absoluteToVisibleColumn(sel);
}
else
{
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+ startx + widthx + 1);
+ while (it.hasNext())
{
-
- res = pos - startx;
-
- if (res < 0 || res > widthx)
- {
- continue;
- }
+ res = it.next() - startx;
gg.fillPolygon(
new int[]
- { -1 + res * avCharWidth - avcharHeight / 4,
- -1 + res * avCharWidth + avcharHeight / 4,
- -1 + res * avCharWidth },
- new int[]
- { y, y, y + 2 * yOf }, 3);
+ { -1 + res * avCharWidth - avcharHeight / 4, -1 + res * avCharWidth + avcharHeight / 4,
+ -1 + res * avCharWidth }, new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Image;
import java.awt.Panel;
import java.beans.PropertyChangeEvent;
-import java.util.List;
+import java.util.Iterator;
public class SeqCanvas extends Panel implements ViewportListenerI
{
if (av.hasHiddenColumns())
{
startx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(startx);
+ .visibleToAbsoluteColumn(startx);
endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
+ .visibleToAbsoluteColumn(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
// WEST SCALE
if (av.hasHiddenColumns())
{
endx = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(endx);
+ .visibleToAbsoluteColumn(endx);
}
SequenceI seq;
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
-
+
FontMetrics fm = getFontMetrics(av.getFont());
-
+
LABEL_EAST = 0;
LABEL_WEST = 0;
-
+
if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
-
+
if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
-
+
int hgap = avcharHeight;
if (av.getScaleAboveWrapped())
{
hgap += avcharHeight;
}
-
+
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
int cHeight = av.getAlignment().getHeight() * avcharHeight;
-
+
av.setWrappedWidth(cWidth);
-
+
av.getRanges().setViewportStartAndWidth(startRes, cWidth);
-
+
int endx;
int ypos = hgap;
-
+
int maxwidth = av.getAlignment().getWidth();
-
+
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
+ .absoluteToVisibleColumn(maxwidth);
}
-
+
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
-
+
if (endx > maxwidth)
{
endx = maxwidth;
}
-
+
g.setColor(Color.black);
-
+
if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
-
+
if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(-(canvasWidth - LABEL_EAST), 0);
}
-
+
g.translate(LABEL_WEST, 0);
-
+
if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
+ endx + 1);
+ while (it.hasNext())
{
- res = pos - startRes;
-
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
-
+ res = it.next() - startRes;
gg.fillPolygon(
new int[]
- { res * avcharWidth - avcharHeight / 4,
- res * avcharWidth + avcharHeight / 4,
- res * avcharWidth },
+ { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
new int[]
- { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2) + 8 },
- 3);
-
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
}
}
-
+
if (g.getClip() == null)
{
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
-
+
drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
-
+
if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
{
annotations = new AnnotationPanel(av);
}
-
+
annotations.drawComponent(g, startRes, endx + 1);
g.translate(0, -cHeight - ypos - 4);
}
g.translate(-LABEL_WEST, 0);
-
+
ypos += cHeight + getAnnotationHeight() + hgap;
-
+
startRes += cWidth;
}
-
+
}
AnnotationPanel annotations;
else
{
int screenY = 0;
- final int screenYMax = endRes - startRes;
- int blockStart = startRes;
- int blockEnd = endRes;
-
- if (av.hasHiddenColumns())
- {
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- for (int[] region : hidden.getHiddenColumnsCopy())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- /*
- * draw up to just before the next hidden region, or the end of
- * the visible region, whichever comes first
- */
- blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
- - screenY);
-
- g1.translate(screenY * avcharWidth, 0);
+ int blockStart;
+ int blockEnd;
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- /*
- * draw the downline of the hidden column marker (ScalePanel draws the
- * triangle on top) if we reached it
- */
- if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
- {
- g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
- 0 + offset,
- (blockEnd - blockStart + 1) * avcharWidth - 1,
- (endSeq - startSeq + 1) * avcharHeight + offset);
- }
-
- g1.translate(-screenY * avcharWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
-
- if (screenY > screenYMax)
- {
- // already rendered last block
- return;
- }
- }
- }
- if (screenY <= screenYMax)
+ while (regions.hasNext())
{
- // remaining visible region to render
- blockEnd = blockStart + (endRes - startRes) - screenY;
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
+
+ /*
+ * draw up to just before the next hidden region, or the end of
+ * the visible region, whichever comes first
+ */
g1.translate(screenY * avcharWidth, 0);
+
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ /*
+ * draw the downline of the hidden column marker (ScalePanel draws the
+ * triangle on top) if we reached it
+ */
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
+ {
+ g1.setColor(Color.blue);
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
+ (endSeq - startSeq + 1) * avcharHeight + offset);
+ }
+
g1.translate(-screenY * avcharWidth, 0);
+ screenY += blockEnd - blockStart + 1;
}
}
-
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
return res;
{
fixedColumns = true;
int y1 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryLeft(startres);
+ .getNextHiddenBoundary(true, startres);
int y2 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryRight(startres);
+ .getNextHiddenBoundary(false, startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
if (sg.getSize() == av.getAlignment().getHeight())
{
if ((av.hasHiddenColumns() && startres < av.getAlignment()
- .getHiddenColumns().getHiddenBoundaryRight(startres)))
+ .getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
{
endEditing();
return;
}
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
- boolean vischange = stretchGroup.recalcConservation(true);
+ boolean vischange = stretchGroup.recalcAnnotations(true);
// here we rely on stretchGroup == av.getSelection()
needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
&& afterDrag;
@Override
public synchronized Enumeration<Object> keys()
{
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
}
}
- /** Called when Jalview is started */
+ /**
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
+ */
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
{
fis = new FileInputStream(propertiesFile);
}
+ applicationProperties.clear();
applicationProperties.load(fis);
// remove any old build properties
* @param obj
* String value of property
*
- * @return String value of property
+ * @return previous value of property (or null)
*/
- public static String setProperty(String key, String obj)
+ public static Object setProperty(String key, String obj)
{
-
+ Object oldValue = null;
try
{
- applicationProperties.setProperty(key, obj);
+ oldValue = applicationProperties.setProperty(key, obj);
if (!propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
System.out.println(
"Error setting property: " + key + " " + obj + "\n" + ex);
}
- return obj;
+ return oldValue;
}
/**
*/
package jalview.bin;
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import javax.swing.UIManager;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
/**
* Main class for Jalview Application <br>
* <br>
*
* @param args
* open <em>filename</em>
+ * @throws InterruptedException
+ * @throws IOException
*/
public static void main(String[] args)
{
/**
* @param args
+ * @throws InterruptedException
+ * @throws IOException
*/
void doMain(String[] args)
{
}
try
{
- Map<String, Object> vbinding = new HashMap<String, Object>();
+ Map<String, Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(nickname);
}
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(data);
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
else
{
param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
- SequenceI repseq = alignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- alignFrame.viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- alignFrame.viewport.getAlignment().setHiddenColumns(cs);
+
+ alignFrame.viewport.getAlignment().setupJPredAlignment();
+
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+ private Hashtable<String, long[]> jshashes = new Hashtable<>();
- private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
- msgset = new Hashtable<String, String[]>();
+ msgset = new Hashtable<>();
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
{
private Alignment dataset;
- protected List<SequenceI> sequences;
+ private List<SequenceI> sequences;
+
+ private SequenceI hmmConsensus;
protected List<SequenceGroup> groups;
return sequences.get(i);
}
}
+
return null;
}
}
/**
+ * Inserts a sequence at a point in the alignment.
+ *
+ * @param i
+ * the index of the position the sequence is to be inserted in.
+ */
+ @Override
+ public void insertSequenceAt(int i, SequenceI snew)
+ {
+ synchronized (sequences)
+ {
+ if (sequences.size() > i)
+ {
+ sequences.add(i, snew);
+ return;
+
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return;
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
if (getSequenceAt(i).getLength() > maxLength)
maxLength = getSequenceAt(i).getLength();
}
}
-
+
return maxLength;
}
+ /*
+ @Override
+ public int getWidth()
+ {
+ final Wrapper temp = new Wrapper();
+
+ forEachSequence(new Consumer<SequenceI>()
+ {
+ @Override
+ public void accept(SequenceI s)
+ {
+ if (s.getLength() > temp.inner)
+ {
+ temp.inner = s.getLength();
+ }
+ }
+ }, 0, sequences.size() - 1);
+
+ return temp.inner;
+ }
+
+ public static class Wrapper
+ {
+ public int inner;
+ }*/
/**
* DOCUMENT ME!
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
annot.hasText = false;
- annot.setCalcId(new String(calcId));
+ if (calcId != null)
+ {
+ annot.setCalcId(calcId);
+ }
annot.autoCalculated = autoCalc;
if (seqRef != null)
{
{
hiddenCols = cols;
}
+
+ @Override
+ public SequenceI getHmmConsensus()
+ {
+ return hmmConsensus;
+ }
+
+ @Override
+ public void setHmmConsensus(SequenceI hmmConsensus)
+ {
+ this.hmmConsensus = hmmConsensus;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator<int[]> it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
}
private long invalidrnastruc = -2;
/**
- * Updates the _rnasecstr field Determines the positions that base pair and
- * the positions of helices based on secondary structure from a Stockholm file
- *
- * @param rnaAnnotation
- */
- private void _updateRnaSecStr(CharSequence rnaAnnotation)
- {
- try
- {
- _rnasecstr = Rna.getHelixMap(rnaAnnotation);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
- {
- // DEBUG System.out.println(px);
- invalidrnastruc = px.getProblemPos();
- }
- if (invalidrnastruc > -1)
- {
- return;
- }
-
- if (_rnasecstr != null && _rnasecstr.length > 0)
- {
- // show all the RNA secondary structure annotation symbols.
- isrna = true;
- showAllColLabels = true;
- scaleColLabel = true;
- _markRnaHelices();
- }
- // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
- }
-
- private void _markRnaHelices()
- {
- int mxval = 0;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < _rnasecstr.length; x++)
- {
-
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- int val = 0;
- try
- {
- val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
- if (mxval < val)
- {
- mxval = val;
- }
- } catch (NumberFormatException q)
- {
- }
- ;
-
- annotations[_rnasecstr[x].getBegin()].value = val;
- annotations[_rnasecstr[x].getEnd()].value = val;
-
- // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
- }
- setScore(mxval);
- }
-
- /**
* map of positions in the associated annotation
*/
private Map<Integer, Annotation> sequenceMapping;
}
}
- /**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * short label shown under sequence labels
- * @param description
- * text displayed on mouseover
- * @param annotations
- * set of positional annotation elements
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations)
- {
- setAnnotationId();
- // always editable?
- editable = true;
- this.label = label;
- this.description = description;
- this.annotations = annotations;
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label
+ * short label shown under sequence labels
+ * @param description
+ * text displayed on mouseover
+ * @param annotations
+ * set of positional annotation elements
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations)
+ {
+ setAnnotationId();
+ // always editable?
+ editable = true;
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+
+ validateRangeAndDisplay();
+ }
+
+ /**
+ * Copy constructor creates a new independent annotation row with the same
+ * associated sequenceRef
+ *
+ * @param annotation
+ */
+ public AlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ setAnnotationId();
+ this.label = new String(annotation.label);
+ if (annotation.description != null)
+ {
+ this.description = new String(annotation.description);
+ }
+ this.graphMin = annotation.graphMin;
+ this.graphMax = annotation.graphMax;
+ this.graph = annotation.graph;
+ this.graphHeight = annotation.graphHeight;
+ this.graphGroup = annotation.graphGroup;
+ this.groupRef = annotation.groupRef;
+ this.editable = annotation.editable;
+ this.autoCalculated = annotation.autoCalculated;
+ this.hasIcons = annotation.hasIcons;
+ this.hasText = annotation.hasText;
+ this.height = annotation.height;
+ this.label = annotation.label;
+ this.padGaps = annotation.padGaps;
+ this.visible = annotation.visible;
+ this.centreColLabels = annotation.centreColLabels;
+ this.scaleColLabel = annotation.scaleColLabel;
+ this.showAllColLabels = annotation.showAllColLabels;
+ this.calcId = annotation.calcId;
+ if (annotation.properties != null)
+ {
+ properties = new HashMap<>();
+ for (Map.Entry<String, String> val : annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
+ if (annotation.threshold != null)
+ {
+ threshold = new GraphLine(annotation.threshold);
+ }
+ Annotation[] ann = annotation.annotations;
+ if (annotation.annotations != null)
+ {
+ this.annotations = new Annotation[ann.length];
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] != null)
+ {
+ annotations[i] = new Annotation(ann[i]);
+ if (_linecolour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
+ }
+ }
+ }
+ if (annotation.sequenceRef != null)
+ {
+ this.sequenceRef = annotation.sequenceRef;
+ if (annotation.sequenceMapping != null)
+ {
+ Integer p = null;
+ sequenceMapping = new HashMap<>();
+ Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+ .iterator();
+ while (pos.hasNext())
+ {
+ // could optimise this!
+ p = pos.next();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
+ {
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] == a)
+ {
+ sequenceMapping.put(p, annotations[i]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ this.sequenceMapping = null;
+ }
+ }
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
+ validateRangeAndDisplay(); // construct hashcodes, etc.
+ }
+
+ /**
+ * copy constructor with edit based on the hidden columns marked in colSel
+ *
+ * @param alignmentAnnotation
+ * @param colSel
+ */
+ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+ HiddenColumns hidden)
+ {
+ this(alignmentAnnotation);
+ if (annotations == null)
+ {
+ return;
+ }
+ makeVisibleAnnotation(hidden);
+ }
+
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param description
+ * DOCUMENT ME!
+ * @param annotations
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ * @param winLength
+ * DOCUMENT ME!
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations, float min, float max, int graphType)
+ {
+ setAnnotationId();
+ // graphs are not editable
+ editable = graphType == 0;
+
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+ graph = graphType;
+ graphMin = min;
+ graphMax = max;
+ validateRangeAndDisplay();
+ }
+
+ /**
+ * Score only annotation
+ *
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
+ }
+
+ /**
+ * Updates the _rnasecstr field Determines the positions that base pair and
+ * the positions of helices based on secondary structure from a Stockholm file
+ *
+ * @param rnaAnnotation
+ */
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
+ {
+ try
+ {
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
+ {
+ // DEBUG System.out.println(px);
+ invalidrnastruc = px.getProblemPos();
+ }
+ if (invalidrnastruc > -1)
+ {
+ return;
+ }
+
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ isrna = true;
+ showAllColLabels = true;
+ scaleColLabel = true;
+ _markRnaHelices();
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
+ }
+
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
- validateRangeAndDisplay();
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
}
/**
}
/**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * DOCUMENT ME!
- * @param description
- * DOCUMENT ME!
- * @param annotations
- * DOCUMENT ME!
- * @param min
- * DOCUMENT ME!
- * @param max
- * DOCUMENT ME!
- * @param winLength
- * DOCUMENT ME!
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max, int graphType)
- {
- setAnnotationId();
- // graphs are not editable
- editable = graphType == 0;
-
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
- graphMin = min;
- graphMax = max;
- validateRangeAndDisplay();
- }
-
- /**
* checks graphMin and graphMax, secondary structure symbols, sets graphType
* appropriately, sets null labels to the empty string if appropriate.
*/
}
/**
- * Copy constructor creates a new independent annotation row with the same
- * associated sequenceRef
- *
- * @param annotation
- */
- public AlignmentAnnotation(AlignmentAnnotation annotation)
- {
- setAnnotationId();
- this.label = new String(annotation.label);
- if (annotation.description != null)
- {
- this.description = new String(annotation.description);
- }
- this.graphMin = annotation.graphMin;
- this.graphMax = annotation.graphMax;
- this.graph = annotation.graph;
- this.graphHeight = annotation.graphHeight;
- this.graphGroup = annotation.graphGroup;
- this.groupRef = annotation.groupRef;
- this.editable = annotation.editable;
- this.autoCalculated = annotation.autoCalculated;
- this.hasIcons = annotation.hasIcons;
- this.hasText = annotation.hasText;
- this.height = annotation.height;
- this.label = annotation.label;
- this.padGaps = annotation.padGaps;
- this.visible = annotation.visible;
- this.centreColLabels = annotation.centreColLabels;
- this.scaleColLabel = annotation.scaleColLabel;
- this.showAllColLabels = annotation.showAllColLabels;
- this.calcId = annotation.calcId;
- if (annotation.properties != null)
- {
- properties = new HashMap<String, String>();
- for (Map.Entry<String, String> val : annotation.properties.entrySet())
- {
- properties.put(val.getKey(), val.getValue());
- }
- }
- if (this.hasScore = annotation.hasScore)
- {
- this.score = annotation.score;
- }
- if (annotation.threshold != null)
- {
- threshold = new GraphLine(annotation.threshold);
- }
- Annotation[] ann = annotation.annotations;
- if (annotation.annotations != null)
- {
- this.annotations = new Annotation[ann.length];
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] != null)
- {
- annotations[i] = new Annotation(ann[i]);
- if (_linecolour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- }
- }
- if (annotation.sequenceRef != null)
- {
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
- {
- Integer p = null;
- sequenceMapping = new HashMap<Integer, Annotation>();
- Iterator<Integer> pos = annotation.sequenceMapping.keySet()
- .iterator();
- while (pos.hasNext())
- {
- // could optimise this!
- p = pos.next();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
- if (ann != null)
- {
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] == a)
- {
- sequenceMapping.put(p, annotations[i]);
- }
- }
- }
- }
- }
- else
- {
- this.sequenceMapping = null;
- }
- }
- // TODO: check if we need to do this: JAL-952
- // if (this.isrna=annotation.isrna)
- {
- // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
- }
- validateRangeAndDisplay(); // construct hashcodes, etc.
- }
-
- /**
* clip the annotation to the columns given by startRes and endRes (inclusive)
* and prune any existing sequenceMapping to just those columns.
*
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> newmapping = new HashMap<>();
Iterator<Integer> e = sequenceMapping.keySet().iterator();
while (e.hasNext())
{
{
return;
}
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
int seqPos;
return hasScore || !Double.isNaN(score);
}
- /**
- * Score only annotation
- *
- * @param label
- * @param description
- * @param score
- */
- public AlignmentAnnotation(String label, String description, double score)
- {
- this(label, description, null);
- setScore(score);
- }
-
- /**
- * copy constructor with edit based on the hidden columns marked in colSel
- *
- * @param alignmentAnnotation
- * @param colSel
- */
- public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- HiddenColumns hidden)
- {
- this(alignmentAnnotation);
- if (annotations == null)
- {
- return;
- }
- hidden.makeVisibleAnnotation(this);
- }
-
public void setPadGaps(boolean padgaps, char gapchar)
{
this.padGaps = padgaps;
/**
* machine readable ID string indicating what generated this annotation
*/
- protected String calcId = "";
+ private String calcId = "";
/**
* properties associated with the calcId
*/
- protected Map<String, String> properties = new HashMap<String, String>();
+ protected Map<String, String> properties = new HashMap<>();
/**
* base colour for line graphs. If null, will be set automatically by
: false;
// TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> mapForsq = new HashMap<>();
if (sequenceMapping != null)
{
if (sp2sq != null)
if (mapping != null)
{
Map<Integer, Annotation> old = sequenceMapping;
- Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> remap = new HashMap<>();
int index = -1;
for (int mp[] : mapping.values())
{
{
if (properties == null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
}
properties.put(property, value);
}
return graphMin < graphMax;
}
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+ }
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ if (annotations != null)
+ {
+ if (hiddenColumns.hasHiddenColumns())
+ {
+ removeHiddenAnnotation(start, end, hiddenColumns);
+ }
+ else
+ {
+ restrict(start, end);
+ }
+ }
+ }
+
+ /**
+ * The actual implementation of deleting hidden annotation columns
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param hiddenColumns
+ * the set of hidden columns
+ */
+ private void removeHiddenAnnotation(int start, int end,
+ HiddenColumns hiddenColumns)
+ {
+ // mangle the alignmentAnnotation annotation array
+ ArrayList<Annotation[]> annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+ end + 1, false);
+
+ int copylength;
+ int annotationLength;
+ while (blocks.hasNext())
+ {
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ if (annotationLength + block[0] <= annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ copylength = annotations.length - block[0];
+ }
+ }
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(annotations, block[0], els, 0, copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, annotations, w, chnk.length);
+ w += chnk.length;
+ }
+ }
+ }
+
public static Iterable<AlignmentAnnotation> findAnnotations(
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
-
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
if ((calcId == null || (ann.getCalcId() != null
public static Iterable<AlignmentAnnotation> findAnnotation(
List<AlignmentAnnotation> list, String calcId)
{
-
List<AlignmentAnnotation> aa = new ArrayList<>();
if (calcId == null)
{
* - null or specific sequence reference
* @param groupRef
* - null or specific group reference
- * @param method
- * - CalcId for the annotation (must match)
*
* @return existing annotation matching the given attributes
*/
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+ /**
+ * Set the hidden columns collection on the alignment
+ *
+ * @param cols
+ */
public void setHiddenColumns(HiddenColumns cols);
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The index of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
+
+ /**
+ * Set the first sequence as representative and hide its insertions. Typically
+ * used when loading JPred files.
+ */
+ public void setupJPredAlignment();
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @param input
+ * alignment view where sequence corresponding to profileseq is first
+ * entry
+ * @return new HiddenColumns for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input);
}
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new ArrayList<SequenceI>();
+ Order = new ArrayList<>();
for (SequenceI seq : orderFrom.getSequences())
{
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
+ Order = new ArrayList<>(Arrays.asList(orderFrom));
}
/**
* alignment, parent group).
*/
AnnotatedCollectionI getContext();
+
+
}
*/
package jalview.datamodel;
-import java.util.List;
+import java.util.Iterator;
public class CigarArray extends CigarBase
{
SequenceGroup selectionGroup)
{
this(constructSeqCigarArray(alignment, selectionGroup));
- constructFromAlignment(alignment,
- hidden != null ? hidden.getHiddenColumnsCopy() : null,
- selectionGroup);
+ constructFromAlignment(alignment, hidden, selectionGroup);
}
private static int[] _calcStartEndBounds(AlignmentI alignment,
* @param selectionGroup
*/
private void constructFromAlignment(AlignmentI alignment,
- List<int[]> list, SequenceGroup selectionGroup)
+ HiddenColumns hidden, SequenceGroup selectionGroup)
{
int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
- int start = _startend[1], end = _startend[2];
+ int start = _startend[1];
+ int end = _startend[2];
// now construct the CigarArray operations
- if (list != null)
+ if (hidden != null)
{
int[] region;
- int hideStart, hideEnd;
+ int hideStart;
+ int hideEnd;
int last = start;
- for (int j = 0; last < end & j < list.size(); j++)
+
+ Iterator<int[]> regions = hidden.getBoundedIterator(start, end);
+ while (regions.hasNext())
{
- region = list.get(j);
+ region = regions.next();
hideStart = region[0];
hideEnd = region[1];
- // edit hidden regions to selection range
-
- // just move on if hideEnd is before last
- if (hideEnd < last)
- {
- continue;
- }
- // exit if next region is after end
- if (hideStart > end)
- {
- break;
- }
// truncate region at start if last falls in region
if ((hideStart < last) && (hideEnd >= last))
addOperation(CigarArray.D, 1 + hideEnd - hideStart);
last = hideEnd + 1;
}
+
// Final match if necessary.
if (last <= end)
{
* List of databases whose sequences might have coding regions annotated
*/
public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
- ENSEMBL };
+ ENSEMBL, ENSEMBLGENOMES };
public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
public static String[] allSources()
{
- List<String> src = new ArrayList<String>();
+ List<String> src = new ArrayList<>();
for (Field f : DBRefSource.class.getFields())
{
if (String.class.equals(f.getType()))
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * stores data for each node in the hmm model
+ * @author TZVanaalten
+ *
+ */
+public class HMMNode
+{
+ //contains the match emissions for each symbol
+ double[] matchEmissions;
+
+ //contains the insert emissions for each symbol
+ double[] insertEmissions;
+
+ // contains the state transitions for each possible transition. These are mm,
+ // mi, md, im, ii, dm and dd in order
+ double[] stateTransitions;
+
+ //annotations
+ int residueNumber;
+ char consensusResidue;
+ char referenceAnnotation;
+ char maskValue;
+ char consensusStructure;
+
+ /**
+ * Constructor
+ */
+ public HMMNode()
+ {
+ }
+
+ public double[] getMatchEmissions()
+ {
+ return matchEmissions;
+ }
+
+ double getMatchEmission(int symbolIndex)
+ {
+ return matchEmissions[symbolIndex];
+ }
+
+ public void setMatchEmissions(double[] matches)
+ {
+ this.matchEmissions = matches;
+ }
+
+ public double[] getInsertEmissions()
+ {
+ return insertEmissions;
+ }
+
+ double getInsertEmission(int symbolIndex)
+ {
+ return insertEmissions[symbolIndex];
+ }
+
+ public void setInsertEmissions(double[] insertEmissionsL)
+ {
+ this.insertEmissions = insertEmissionsL;
+ }
+
+ public double[] getStateTransitions()
+ {
+ return stateTransitions;
+ }
+
+ double getStateTransition(int transition)
+ {
+ return stateTransitions[transition];
+ }
+
+ public void setStateTransitions(double[] stateTransitionsM)
+ {
+ this.stateTransitions = stateTransitionsM;
+ }
+
+ int getResidueNumber()
+ {
+ return residueNumber;
+ }
+ public void setResidueNumber(int resNo)
+ {
+ this.residueNumber = resNo;
+ }
+
+ char getConsensusResidue()
+ {
+ return consensusResidue;
+ }
+ public void setConsensusResidue(char consensusResidue)
+ {
+ this.consensusResidue = consensusResidue;
+ }
+
+ char getReferenceAnnotation()
+ {
+ return referenceAnnotation;
+ }
+ public void setReferenceAnnotation(char referenceAnnotation)
+ {
+ this.referenceAnnotation = referenceAnnotation;
+ }
+
+ char getMaskValue()
+ {
+ return maskValue;
+ }
+ public void setMaskValue(char maskValue)
+ {
+ this.maskValue = maskValue;
+ }
+
+ char getConsensusStructure()
+ {
+ return consensusStructure;
+ }
+ public void setConsensusStructure(char consensusStructure)
+ {
+ this.consensusStructure = consensusStructure;
+ }
+
+ /**
+ * Answers the symbol index of the symbol with the highest match emission
+ * probability (first symbol in case of a tie). Note this object stores
+ * probabilities, not the negative logarithms as in the HMM file.
+ *
+ * @return
+ */
+ int getMaxMatchEmissionIndex()
+ {
+ int maxIndex = 0;
+ double max = 0D;
+
+ for (int i = 0; i < matchEmissions.length; i++)
+ {
+ if (matchEmissions[i] > max)
+ {
+ max = matchEmissions[i];
+ maxIndex = i;
+ }
+ }
+ return maxIndex;
+ }
+}
+
+
*/
package jalview.datamodel;
-import jalview.util.Comparison;
-import jalview.util.ShiftList;
-
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.BitSet;
-import java.util.Collections;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import java.util.concurrent.locks.ReentrantReadWriteLock;
+/**
+ * This class manages the collection of hidden columns associated with an
+ * alignment. To iterate over the collection, or over visible columns/regions,
+ * use an iterator obtained from one of:
+ *
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning *absolute* positions
+ *
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning *visible* positions
+ *
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
+ * *absolute* positions
+ *
+ * - getVisibleColsIterator: iterates over the visible *columns*
+ *
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
+ *
+ * @author kmourao
+ */
+
+/* Implementation notes:
+ *
+ * Methods which change the hiddenColumns collection should use a writeLock to
+ * prevent other threads accessing the hiddenColumns collection while changes
+ * are being made. They should also reset the hidden columns cursor, and either
+ * update the hidden columns count, or set it to 0 (so that it will later be
+ * updated when needed).
+ *
+ *
+ * Methods which only need read access to the hidden columns collection should
+ * use a readLock to prevent other threads changing the hidden columns
+ * collection while it is in use.
+ */
public class HiddenColumns
{
+ private static final int HASH_MULTIPLIER = 31;
+
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
/*
+ * Cursor which tracks the last used hidden columns region, and the number
+ * of hidden columns up to (but not including) that region.
+ */
+ private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+ /*
+ * cache of the number of hidden columns: must be kept up to date by methods
+ * which add or remove hidden columns
+ */
+ private int numColumns = 0;
+
+ /*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
- private ArrayList<int[]> hiddenColumns;
+ private List<int[]> hiddenColumns = new ArrayList<>();
/**
* Constructor
* Copy constructor
*
* @param copy
+ * the HiddenColumns object to copy from
*/
public HiddenColumns(HiddenColumns copy)
{
+ this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
+ }
+
+ /**
+ * Copy constructor within bounds and with offset. Copies hidden column
+ * regions fully contained between start and end, and offsets positions by
+ * subtracting offset.
+ *
+ * @param copy
+ * HiddenColumns instance to copy from
+ * @param start
+ * lower bound to copy from
+ * @param end
+ * upper bound to copy to
+ * @param offset
+ * offset to subtract from each region boundary position
+ *
+ */
+ public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
+ {
try
{
LOCK.writeLock().lock();
if (copy != null)
{
- if (copy.hiddenColumns != null)
+ numColumns = 0;
+ Iterator<int[]> it = copy.getBoundedIterator(start, end);
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ // still need to check boundaries because iterator returns
+ // all overlapping regions and we need contained regions
+ if (region[0] >= start && region[1] <= end)
+ {
+ hiddenColumns.add(
+ new int[]
+ { region[0] - offset, region[1] - offset });
+ numColumns += region[1] - region[0] + 1;
+ }
+ }
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Adds the specified column range to the hidden columns collection
+ *
+ * @param start
+ * start of range to add (absolute position in alignment)
+ * @param end
+ * end of range to add (absolute position in alignment)
+ */
+ public void hideColumns(int start, int end)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
+ if (!hiddenColumns.isEmpty())
+ {
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
+ {
+ // get previous index and hidden count for updating the cursor later
+ previndex = regionindex - 1;
+ int[] prevRegion = hiddenColumns.get(previndex);
+ prevHiddenCount = cursorPos.getHiddenSoFar()
+ - (prevRegion[1] - prevRegion[0] + 1);
+ }
+ }
+
+ // new range follows everything else; check first to avoid looping over
+ // whole hiddenColumns collection
+ if (hiddenColumns.isEmpty()
+ || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
+ {
+ hiddenColumns.add(new int[] { start, end });
+ numColumns += end - start + 1;
+ }
+ else
+ {
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ boolean added = false;
+ if (regionindex > 0)
+ {
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
+ {
+ insertRangeAtRegion(regionindex, start, end);
+ }
+ }
+
+ // reset the cursor to just before our insertion point: this saves
+ // a lot of reprocessing in large alignments
+ cursor = new HiddenColumnsCursor(hiddenColumns, previndex,
+ prevHiddenCount);
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
+ *
+ * @param i
+ * index to insert at
+ * @param start
+ * start of range to insert
+ * @param end
+ * end of range to insert
+ * @return true if range was successfully inserted
+ */
+ private boolean insertRangeAtRegion(int i, int start, int end)
+ {
+ boolean added = false;
+
+ int[] region = hiddenColumns.get(i);
+ if (end < region[0] - 1)
+ {
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.add(i, new int[] { start, end });
+ numColumns += end - start + 1;
+ added = true;
+ }
+ else if (end <= region[1])
+ {
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ int oldstart = region[0];
+ region[0] = Math.min(region[0], start);
+ numColumns += oldstart - region[0]; // new columns are between old and
+ // adjusted starts
+ added = true;
+ }
+ else if (start <= region[1] + 1)
+ {
+ /*
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
+ */
+ insertRangeAtOverlap(i, start, end, region);
+ added = true;
+ }
+ return added;
+ }
+
+ /**
+ * Insert a range whose start position overlaps an existing region and/or is
+ * contiguous to the right of the region
+ *
+ * @param i
+ * index to insert at
+ * @param start
+ * start of range to insert
+ * @param end
+ * end of range to insert
+ * @param region
+ * the overlapped/continued region
+ */
+ private void insertRangeAtOverlap(int i, int start, int end, int[] region)
+ {
+ int oldstart = region[0];
+ int oldend = region[1];
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
+
+ numColumns += oldstart - region[0];
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ int endi = i;
+ while (endi < hiddenColumns.size() - 1)
+ {
+ int[] nextRegion = hiddenColumns.get(endi + 1);
+ if (nextRegion[0] > end + 1)
+ {
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
+ }
+ numColumns -= nextRegion[1] - nextRegion[0] + 1;
+ region[1] = Math.max(nextRegion[1], end);
+ endi++;
+ }
+ numColumns += region[1] - oldend;
+ hiddenColumns.subList(i + 1, endi + 1).clear();
+ }
+
+ /**
+ * hide a list of ranges
+ *
+ * @param ranges
+ */
+ public void hideList(List<int[]> ranges)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+ for (int[] r : ranges)
+ {
+ hideColumns(r[0], r[1]);
+ }
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Unhides, and adds to the selection list, all hidden columns
+ */
+ public void revealAllHiddenColumns(ColumnSelection sel)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ for (int[] region : hiddenColumns)
+ {
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList();
+ sel.addElement(j);
}
}
+ hiddenColumns.clear();
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ numColumns = 0;
+
} finally
{
LOCK.writeLock().unlock();
}
/**
- * This method is used to return all the HiddenColumn regions and is intended
- * to remain private. External callers which need a copy of the regions can
- * call getHiddenColumnsCopyAsList.
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
*
- * @return empty list or List of hidden column intervals
+ * @param start
+ * the start column to look for
+ * @param sel
+ * the column selection to add the hidden column range to
*/
- private List<int[]> getHiddenRegions()
+ public void revealHiddenColumns(int start, ColumnSelection sel)
{
- return hiddenColumns == null ? Collections.<int[]> emptyList()
- : hiddenColumns;
+ try
+ {
+ LOCK.writeLock().lock();
+
+ if (!hiddenColumns.isEmpty())
+ {
+ int regionIndex = cursor.findRegionForColumn(start, false)
+ .getRegionIndex();
+
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
+ {
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
+ {
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
+ numColumns -= colsToRemove;
+ }
+ }
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
}
/**
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+
+ boolean first = true;
+ for (int[] range : hiddenColumns)
{
- for (int[] range : hiddenColumns)
+ if (!first)
+ {
+ regionBuilder.append(delimiter);
+ }
+ else
{
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
+ first = false;
}
+ regionBuilder.append(range[0]).append(between).append(range[1]);
- regionBuilder.deleteCharAt(0);
}
+
return regionBuilder.toString();
} finally
{
*/
public int getSize()
{
+ return numColumns;
+ }
+
+ /**
+ * Get the number of distinct hidden regions
+ *
+ * @return number of regions
+ */
+ public int getNumberOfRegions()
+ {
try
{
LOCK.readLock().lock();
- int size = 0;
- if (hasHiddenColumns())
- {
- for (int[] range : hiddenColumns)
- {
- size += range[1] - range[0] + 1;
- }
- }
- return size;
+ return hiddenColumns.size();
} finally
{
LOCK.readLock().unlock();
/*
* check hidden columns are either both null, or match
*/
- if (this.hiddenColumns == null)
- {
- return (that.hiddenColumns == null);
- }
- if (that.hiddenColumns == null
- || that.hiddenColumns.size() != this.hiddenColumns.size())
+
+ if (that.hiddenColumns.size() != this.hiddenColumns.size())
{
return false;
}
- int i = 0;
- for (int[] thisRange : hiddenColumns)
+
+ Iterator<int[]> it = this.iterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
{
- int[] thatRange = that.hiddenColumns.get(i++);
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ if (!(Arrays.equals(it.next(), thatit.next())))
{
return false;
}
}
return true;
+
} finally
{
LOCK.readLock().unlock();
* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
- public int adjustForHiddenColumns(int column)
+ public int visibleToAbsoluteColumn(int column)
{
try
{
LOCK.readLock().lock();
int result = column;
- if (hiddenColumns != null)
+
+ if (!hiddenColumns.isEmpty())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
+ result += cursor.findRegionForColumn(column, true)
+ .getHiddenSoFar();
}
+
return result;
} finally
{
/**
* Use this method to find out where a column will appear in the visible
* alignment when hidden columns exist. If the column is not visible, then the
- * left-most visible column will always be returned.
+ * index of the next visible column on the left will be returned (or 0 if
+ * there is no visible column on the left)
*
* @param hiddenColumn
* the column index in the full alignment including hidden columns
* @return the position of the column in the visible alignment
*/
- public int findColumnPosition(int hiddenColumn)
+ public int absoluteToVisibleColumn(int hiddenColumn)
{
try
{
LOCK.readLock().lock();
int result = hiddenColumn;
- if (hiddenColumns != null)
- {
- int index = 0;
- int[] region;
- do
- {
- region = hiddenColumns.get(index++);
- if (hiddenColumn > region[1])
- {
- result -= region[1] + 1 - region[0];
- }
- } while ((hiddenColumn > region[1])
- && (index < hiddenColumns.size()));
- if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+ if (!hiddenColumns.isEmpty())
+ {
+ HiddenCursorPosition cursorPos = cursor
+ .findRegionForColumn(hiddenColumn, false);
+ int index = cursorPos.getRegionIndex();
+ int hiddenBeforeCol = cursorPos.getHiddenSoFar();
+
+ // just subtract hidden cols count - this works fine if column is
+ // visible
+ result = hiddenColumn - hiddenBeforeCol;
+
+ // now check in case column is hidden - it will be in the returned
+ // hidden region
+ if (index < hiddenColumns.size())
{
- // Here the hidden column is within a region, so
- // we want to return the position of region[0]-1, adjusted for any
- // earlier hidden columns.
- // Calculate the difference between the actual hidden col position
- // and region[0]-1, and then subtract from result to convert result
- // from
- // the adjusted hiddenColumn value to the adjusted region[0]-1 value
-
- // However, if the region begins at 0 we cannot return region[0]-1
- // just return 0
- if (region[0] == 0)
- {
- return 0;
- }
- else
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- return result - (hiddenColumn - region[0] + 1);
+ // actually col is hidden, return region[0]-1
+ // unless region[0]==0 in which case return 0
+ if (region[0] == 0)
+ {
+ result = 0;
+ }
+ else
+ {
+ result = region[0] - 1 - hiddenBeforeCol;
+ }
}
}
}
+
return result; // return the shifted position after removing hidden
// columns.
} finally
/**
* Find the visible column which is a given visible number of columns to the
- * left of another visible column. i.e. for a startColumn x, the column which
- * is distance 1 away will be column x-1.
+ * left (negative visibleDistance) or right (positive visibleDistance) of
+ * startColumn. If startColumn is not visible, we use the visible column at
+ * the left boundary of the hidden region containing startColumn.
*
* @param visibleDistance
- * the number of visible columns to offset by
+ * the number of visible columns to offset by (left offset = negative
+ * value; right offset = positive value)
* @param startColumn
- * the column to start from
- * @return the position of the column in the visible alignment
+ * the position of the column to start from (absolute position)
+ * @return the position of the column which is <visibleDistance> away
+ * (absolute position)
*/
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
+ public int offsetByVisibleColumns(int visibleDistance, int startColumn)
{
try
{
-
LOCK.readLock().lock();
- int distance = visibleDistance;
-
- // in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
-
- // get index of hidden region to left of start
- int index = getHiddenIndexLeft(start);
- if (index == -1)
- {
- // no hidden regions to left of startColumn
- return start - distance;
- }
-
- // walk backwards through the alignment subtracting the counts of visible
- // columns from distance
- int[] region;
- int gap = 0;
- int nextstart = start;
-
- while ((index > -1) && (distance - gap > 0))
- {
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
-
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
-
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
- }
+ int start = absoluteToVisibleColumn(startColumn);
+ return visibleToAbsoluteColumn(start + visibleDistance);
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
- }
- return start - distance;
} finally
{
LOCK.readLock().unlock();
}
-
}
/**
- * Use this method to determine the set of hiddenRegion start positions
+ * This method returns the rightmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the next hidden column.
*
- * @return list of column number in visible view where hidden regions start
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
+ * @return the index of the next hidden column, or alPos if there is no next
+ * hidden column
*/
- public List<Integer> findHiddenRegionPositions()
+ public int getNextHiddenBoundary(boolean left, int alPos)
{
try
{
LOCK.readLock().lock();
- List<Integer> positions = null;
-
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
- positions = new ArrayList<>(hiddenColumns.size());
+ int index = cursor.findRegionForColumn(alPos, false)
+ .getRegionIndex();
- positions.add(hiddenColumns.get(0)[0]);
- for (int i = 1; i < hiddenColumns.size(); ++i)
+ if (left && index > 0)
{
-
- int result = 0;
- if (hiddenColumns != null)
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
+ else if (!left && index < hiddenColumns.size())
+ {
+ int[] region = hiddenColumns.get(index);
+ if (alPos < region[0])
{
- int index = 0;
- int gaps = 0;
- do
- {
- int[] region = hiddenColumns.get(index);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= i);
-
- result -= gaps;
+ return region[0];
+ }
+ else if ((alPos <= region[1])
+ && (index + 1 < hiddenColumns.size()))
+ {
+ // alPos is within a hidden region, return the next one
+ // if there is one
+ region = hiddenColumns.get(index + 1);
+ return region[0];
}
- positions.add(result);
}
}
- else
- {
- positions = new ArrayList<>();
- }
-
- return positions;
+ return alPos;
} finally
{
LOCK.readLock().unlock();
}
/**
- * This method returns the rightmost limit of a region of an alignment with
- * hidden columns. In otherwords, the next hidden column.
+ * Answers if a column in the alignment is visible
*
- * @param index
- * int
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
*/
- public int getHiddenBoundaryRight(int alPos)
+ public boolean isVisible(int column)
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+
+ if (!hiddenColumns.isEmpty())
{
- int index = 0;
- do
+ int regionindex = cursor.findRegionForColumn(column, false)
+ .getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- int[] region = hiddenColumns.get(index);
- if (alPos < region[0])
+ int[] region = hiddenColumns.get(regionindex);
+ // already know that column <= region[1] as cursor returns containing
+ // region or region to right
+ if (column >= region[0])
{
- return region[0];
+ return false;
}
-
- index++;
- } while (index < hiddenColumns.size());
+ }
}
+ return true;
- return alPos;
} finally
{
LOCK.readLock().unlock();
}
-
}
/**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
*
- * @param index
- * int
+ * @return true if there are columns hidden
*/
- public int getHiddenBoundaryLeft(int alPos)
+ public boolean hasHiddenColumns()
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
- }
-
- return alPos;
+ // we don't use getSize()>0 here because it has to iterate over
+ // the full hiddenColumns collection and so will be much slower
+ return (!hiddenColumns.isEmpty());
} finally
{
LOCK.readLock().unlock();
}
/**
- * This method returns the index of the hidden region to the left of a column
- * position. If the column is in a hidden region it returns the index of the
- * region to the left. If there is no hidden region to the left it returns -1.
*
- * @param pos
- * int
+ * @return true if there is more than one hidden column region
*/
- private int getHiddenIndexLeft(int pos)
+ public boolean hasMultiHiddenColumnRegions()
{
try
{
-
LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
- }
-
- return -1;
+ return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
} finally
{
LOCK.readLock().unlock();
}
-
}
+
/**
- * Adds the specified column range to the hidden columns
- *
- * @param start
- * @param end
+ * Returns a hashCode built from hidden column ranges
*/
- public void hideColumns(int start, int end)
+ @Override
+ public int hashCode()
{
- boolean wasAlreadyLocked = false;
try
{
- // check if the write lock was already locked by this thread,
- // as this method can be called internally in loops within HiddenColumns
- if (!LOCK.isWriteLockedByCurrentThread())
- {
- LOCK.writeLock().lock();
- }
- else
- {
- wasAlreadyLocked = true;
- }
-
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<>();
- }
+ LOCK.readLock().lock();
+ int hashCode = 1;
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- for (int i = 0; i < hiddenColumns.size(); i++)
+ for (int[] hidden : hiddenColumns)
{
- int[] region = hiddenColumns.get(i);
-
- if (end < region[0] - 1)
- {
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.add(i, new int[] { start, end });
- return;
- }
-
- if (end <= region[1])
- {
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- return;
- }
-
- if (start <= region[1] + 1)
- {
- /*
- * new range overlaps existing, or is contiguous following it - adjust
- * start and end columns
- */
- region[0] = Math.min(region[0], start);
- region[1] = Math.max(region[1], end);
-
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
- {
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
- {
- /*
- * gap to next hidden range - no more to update
- */
- break;
- }
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
- }
- return;
- }
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
-
- /*
- * remaining case is that the new range follows everything else
- */
- hiddenColumns.add(new int[] { start, end });
+ return hashCode;
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ LOCK.readLock().unlock();
}
}
- public boolean isVisible(int column)
+ /**
+ * Hide columns corresponding to the marked bits
+ *
+ * @param inserts
+ * - columns mapped to bits starting from zero
+ */
+ public void hideColumns(BitSet inserts)
+ {
+ hideColumns(inserts, 0, inserts.length() - 1);
+ }
+
+ /**
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ *
+ * @param tohide
+ * columns mapped to bits starting from zero
+ * @param start
+ * start of range to hide columns within
+ * @param end
+ * end of range to hide columns within
+ */
+ private void hideColumns(BitSet tohide, int start, int end)
{
try
{
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
+ LOCK.writeLock().lock();
+ for (int firstSet = tohide
+ .nextSetBit(start), lastSet = start; firstSet >= start
+ && lastSet <= end; firstSet = tohide
+ .nextSetBit(lastSet))
{
- for (int[] region : hiddenColumns)
+ lastSet = tohide.nextClearBit(firstSet);
+ if (lastSet <= end)
{
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
+ hideColumns(firstSet, lastSet - 1);
+ }
+ else if (firstSet <= end)
+ {
+ hideColumns(firstSet, end);
}
}
-
- return true;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
} finally
{
- LOCK.readLock().unlock();
- }
- }
-
- private ArrayList<int[]> copyHiddenRegionsToArrayList()
- {
- int size = 0;
- if (hiddenColumns != null)
- {
- size = hiddenColumns.size();
- }
- ArrayList<int[]> copy = new ArrayList<>(size);
-
- for (int i = 0, j = size; i < j; i++)
- {
- int[] rh;
- int[] cp;
- rh = hiddenColumns.get(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- copy.add(cp);
- }
+ LOCK.writeLock().unlock();
}
-
- return copy;
}
/**
- * Returns a copy of the vector of hidden regions, as an ArrayList. Before
- * using this method please consider if you really need access to the hidden
- * regions - a new (or existing!) method on HiddenColumns might be more
- * appropriate.
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ * NB Existing entries in [start,end] are cleared.
*
- * @return hidden regions as an ArrayList of [start,end] pairs
+ * @param tohide
+ * columns mapped to bits starting from zero
+ * @param start
+ * start of range to hide columns within
+ * @param end
+ * end of range to hide columns within
*/
- public ArrayList<int[]> getHiddenColumnsCopy()
+ public void clearAndHideColumns(BitSet tohide, int start, int end)
{
- try
- {
- LOCK.readLock().lock();
- return copyHiddenRegionsToArrayList();
- } finally
- {
- LOCK.readLock().unlock();
- }
+ clearHiddenColumnsInRange(start, end);
+ hideColumns(tohide, start, end);
}
/**
- * propagate shift in alignment columns to column selection
+ * Make all columns in the range [start,end] visible
*
* @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * start of range to show columns
+ * @param end
+ * end of range to show columns
*/
- public List<int[]> compensateForEdit(int start, int change,
- ColumnSelection sel)
+ private void clearHiddenColumnsInRange(int start, int end)
{
try
{
LOCK.writeLock().lock();
- List<int[]> deletedHiddenColumns = null;
-
- if (hiddenColumns != null)
+
+ if (!hiddenColumns.isEmpty())
{
- deletedHiddenColumns = new ArrayList<>();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
+ int index = pos.getRegionIndex();
+
+ if (index != -1 && index != hiddenColumns.size())
{
- int[] region = hiddenColumns.get(i);
- if (region[0] > start && start + change > region[1])
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(index);
+ if (region[0] < start && region[1] >= start)
{
- deletedHiddenColumns.add(region);
-
- hiddenColumns.remove(i);
- i--;
- hSize--;
- continue;
+ // region contains start, truncate so that it ends just before start
+ numColumns -= region[1] - start + 1;
+ region[1] = start - 1;
+ index++;
}
- if (region[0] > start)
+ int endi = index;
+ while (endi < hiddenColumns.size())
{
- region[0] -= change;
- region[1] -= change;
- }
+ region = hiddenColumns.get(endi);
- if (region[0] < 0)
- {
- region[0] = 0;
+ if (region[1] > end)
+ {
+ if (region[0] <= end)
+ {
+ // region contains end, truncate so it starts just after end
+ numColumns -= end - region[0] + 1;
+ region[0] = end + 1;
+ }
+ break;
+ }
+
+ numColumns -= region[1] - region[0] + 1;
+ endi++;
}
+ hiddenColumns.subList(index, endi).clear();
}
- this.revealHiddenColumns(0, sel);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
}
-
- return deletedHiddenColumns;
} finally
{
LOCK.writeLock().unlock();
}
/**
- * propagate shift in alignment columns to column selection special version of
- * compensateForEdit - allowing for edits within hidden regions
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @param updates
+ * BitSet where hidden columns will be marked
*/
- public void compensateForDelEdits(int start, int change)
+ protected void andNot(BitSet updates)
{
try
{
LOCK.writeLock().lock();
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- if (region[0] >= start)
- {
- region[0] -= change;
- }
- if (region[1] >= start)
- {
- region[1] -= change;
- }
- if (region[1] < region[0])
- {
- hiddenColumns.remove(i--);
- }
- if (region[0] < 0)
- {
- region[0] = 0;
- }
- if (region[1] < 0)
- {
- region[1] = 0;
- }
- }
+ BitSet hiddenBitSet = new BitSet();
+ for (int[] range : hiddenColumns)
+ {
+ hiddenBitSet.set(range[0], range[1] + 1);
}
+ hiddenBitSet.andNot(updates);
+ hiddenColumns.clear();
+ hideColumns(hiddenBitSet);
} finally
{
LOCK.writeLock().unlock();
}
/**
- * return all visible segments between the given start and end boundaries
+ * Calculate the visible start and end index of an alignment.
*
- * @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
- * @return int[] {i_start, i_end, ..} where intervals lie in
- * start<=i_start<=i_end<end
+ * @param width
+ * full alignment width
+ * @return integer array where: int[0] = startIndex, and int[1] = endIndex
*/
- public int[] getVisibleContigs(int start, int end)
+ public int[] getVisibleStartAndEndIndex(int width)
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- List<int[]> visiblecontigs = new ArrayList<>();
- List<int[]> regions = getHiddenRegions();
- int vstart = start;
- int[] region;
- int hideStart;
- int hideEnd;
+ int firstVisible = 0;
+ int lastVisible = width - 1;
- for (int j = 0; vstart < end && j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- visiblecontigs.add(new int[] { vstart, hideStart - 1 });
- }
- vstart = hideEnd + 1;
- }
+ if (!hiddenColumns.isEmpty())
+ {
+ // first visible col with index 0, convert to absolute index
+ firstVisible = visibleToAbsoluteColumn(0);
- if (vstart < end)
+ // last visible column is either immediately to left of
+ // last hidden region, or is just the last column in the alignment
+ int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1);
+ if (lastregion[1] == width - 1)
{
- visiblecontigs.add(new int[] { vstart, end - 1 });
+ // last region is at very end of alignment
+ // last visible column immediately precedes it
+ lastVisible = lastregion[0] - 1;
}
- int[] vcontigs = new int[visiblecontigs.size() * 2];
- for (int i = 0, j = visiblecontigs.size(); i < j; i++)
- {
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
- }
- visiblecontigs.clear();
- return vcontigs;
- }
- else
- {
- return new int[] { start, end - 1 };
}
+ return new int[] { firstVisible, lastVisible };
+
} finally
{
LOCK.readLock().unlock();
}
}
- public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
+ /**
+ * Finds the hidden region (if any) which starts or ends at res
+ *
+ * @param res
+ * visible residue position, unadjusted for hidden columns
+ * @return region as [start,end] or null if no matching region is found. If
+ * res is adjacent to two regions, returns the left region.
+ */
+ public int[] getRegionWithEdgeAtRes(int res)
{
try
{
LOCK.readLock().lock();
- int iSize = seqs.length;
- String[] selections = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- for (int i = 0; i < iSize; i++)
- {
- StringBuffer visibleSeq = new StringBuffer();
- List<int[]> regions = getHiddenRegions();
-
- int blockStart = start;
- int blockEnd = end;
- int[] region;
- int hideStart;
- int hideEnd;
+ int adjres = visibleToAbsoluteColumn(res);
- for (int j = 0; j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
- }
+ int[] reveal = null;
- selections[i] = visibleSeq.toString();
- }
- }
- else
+ if (!hiddenColumns.isEmpty())
{
- for (int i = 0; i < iSize; i++)
+ // look for a region ending just before adjres
+ int regionindex = cursor.findRegionForColumn(adjres - 1, false)
+ .getRegionIndex();
+ if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[1] == adjres - 1)
+ {
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
{
- selections[i] = seqs[i].getSequenceAsString(start, end);
+ reveal = hiddenColumns.get(regionindex);
}
}
+ return reveal;
- return selections;
} finally
{
LOCK.readLock().unlock();
}
/**
- * Locate the first and last position visible for this sequence. if seq isn't
- * visible then return the position of the left and right of the hidden
- * boundary region, and the corresponding alignment column indices for the
- * extent of the sequence
- *
- * @param seq
- * @return int[] { visible start, visible end, first seqpos, last seqpos,
- * alignment index for seq start, alignment index for seq end }
+ * Return an iterator over the hidden regions
*/
- public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+ public Iterator<int[]> iterator()
{
try
{
LOCK.readLock().lock();
- int fpos = seq.getStart();
- int lpos = seq.getEnd();
- int start = 0;
-
- if (hiddenColumns == null || hiddenColumns.size() == 0)
- {
- int ifpos = seq.findIndex(fpos) - 1;
- int ilpos = seq.findIndex(lpos) - 1;
- return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
- }
-
- // Simply walk along the sequence whilst watching for hidden column
- // boundaries
- List<int[]> regions = getHiddenRegions();
- int spos = fpos;
- int lastvispos = -1;
- int rcount = 0;
- int hideStart = seq.getLength();
- int hideEnd = -1;
- int visPrev = 0;
- int visNext = 0;
- int firstP = -1;
- int lastP = -1;
- boolean foundStart = false;
- for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
- && p < pLen; p++)
- {
- if (!Comparison.isGap(seq.getCharAt(p)))
- {
- // keep track of first/last column
- // containing sequence data regardless of visibility
- if (firstP == -1)
- {
- firstP = p;
- }
- lastP = p;
- // update hidden region start/end
- while (hideEnd < p && rcount < regions.size())
- {
- int[] region = regions.get(rcount++);
- visPrev = visNext;
- visNext += region[0] - visPrev;
- hideStart = region[0];
- hideEnd = region[1];
- }
- if (hideEnd < p)
- {
- hideStart = seq.getLength();
- }
- // update visible boundary for sequence
- if (p < hideStart)
- {
- if (!foundStart)
- {
- fpos = spos;
- start = p;
- foundStart = true;
- }
- lastvispos = p;
- lpos = spos;
- }
- // look for next sequence position
- spos++;
- }
- }
- if (foundStart)
- {
- return new int[] { findColumnPosition(start),
- findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
- }
- // otherwise, sequence was completely hidden
- return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+ return new RangeIterator(hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * Return a bounded iterator over the hidden regions
*
- * @param alignmentAnnotation
+ * @param start
+ * position to start from (inclusive, absolute column position)
+ * @param end
+ * position to end at (inclusive, absolute column position)
+ * @return
*/
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+ public Iterator<int[]> getBoundedIterator(int start, int end)
{
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ try
+ {
+ LOCK.readLock().lock();
+ return new RangeIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * Return a bounded iterator over the *visible* start positions of hidden
+ * regions
*
* @param start
- * remove any annotation to the right of this column
+ * position to start from (inclusive, visible column position)
* @param end
- * remove any annotation to the left of this column
- * @param alignmentAnnotation
- * the annotation to operate on
+ * position to end at (inclusive, visible column position)
*/
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ public Iterator<Integer> getStartRegionIterator(int start, int end)
{
try
{
LOCK.readLock().lock();
- if (alignmentAnnotation.annotations == null)
- {
- return;
- }
- if (start == end && end == -1)
- {
- start = 0;
- end = alignmentAnnotation.annotations.length;
- }
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- // then mangle the alignmentAnnotation annotation array
- Vector<Annotation[]> annels = new Vector<>();
- Annotation[] els = null;
- List<int[]> regions = getHiddenRegions();
- int blockStart = start;
- int blockEnd = end;
- int[] region;
- int hideStart;
- int hideEnd;
- int w = 0;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- annels.addElement(els = new Annotation[blockEnd - blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
- if (end > blockStart)
- {
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length
- + blockStart) <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
- }
- else
- {
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
- }
- w += els.length;
- }
- if (w == 0)
- {
- return;
- }
+ // get absolute position of column in alignment
+ int absoluteStart = visibleToAbsoluteColumn(start);
- alignmentAnnotation.annotations = new Annotation[w];
- w = 0;
+ // Get cursor position and supply it to the iterator:
+ // Since we want visible region start, we look for a cursor for the
+ // (absoluteStart-1), then if absoluteStart is the start of a visible
+ // region we'll get the cursor pointing to the region before, which is
+ // what we want
+ HiddenCursorPosition pos = cursor
+ .findRegionForColumn(absoluteStart - 1, false);
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
- }
- }
- else
- {
- alignmentAnnotation.restrict(start, end);
- }
+ return new StartRegionIterator(pos, start, end,
+ hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
/**
+ * Return an iterator over visible *columns* (not regions) between the given
+ * start and end boundaries
*
- * @return true if there are columns hidden
+ * @param start
+ * first column (inclusive)
+ * @param end
+ * last column (inclusive)
*/
- public boolean hasHiddenColumns()
+ public Iterator<Integer> getVisibleColsIterator(int start, int end)
{
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 0;
+ return new RangeElementsIterator(
+ new VisibleContigsIterator(start, end + 1, hiddenColumns));
} finally
{
LOCK.readLock().unlock();
}
/**
+ * return an iterator over visible segments between the given start and end
+ * boundaries
*
- * @return true if there are more than one set of columns hidden
+ * @param start
+ * first column, inclusive from 0
+ * @param end
+ * last column - not inclusive
+ * @param useVisibleCoords
+ * if true, start and end are visible column positions, not absolute
+ * positions*
*/
- public boolean hasManyHiddenColumns()
+ public VisibleContigsIterator getVisContigsIterator(int start,
+ int end,
+ boolean useVisibleCoords)
{
+ int adjstart = start;
+ int adjend = end;
+ if (useVisibleCoords)
+ {
+ adjstart = visibleToAbsoluteColumn(start);
+ adjend = visibleToAbsoluteColumn(end);
+ }
+
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 1;
+ return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
}
-
- /**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
- *
- * @param sr
- */
- public void hideInsertionsFor(SequenceI sr)
- {
- try
- {
- LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
- {
- hideColumns(r[0], r[1]);
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Unhides, and adds to the selection list, all hidden columns
- */
- public void revealAllHiddenColumns(ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
- }
- }
-
- hiddenColumns = null;
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
- *
- * @param start
- */
- public void revealHiddenColumns(int start, ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- if (start == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
-
- hiddenColumns.remove(region);
- break;
- }
- }
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
- *
- * @param shifts
- * @param intervals
- * @return
- */
- private boolean pruneIntervalList(final List<int[]> shifts,
- ArrayList<int[]> intervals)
- {
- boolean pruned = false;
- int i = 0;
- int j = intervals.size() - 1;
- int s = 0;
- int t = shifts.size() - 1;
- int[] hr = intervals.get(i);
- int[] sr = shifts.get(s);
- while (i <= j && s <= t)
- {
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
- {
- if (i < j)
- {
- hr = intervals.get(++i);
- }
- else
- {
- i++;
- }
- continue;
- }
- int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
- if (endshift < hr[0] || endshift < sr[0])
- { // leadinghc disjoint or not a deletion
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- boolean leadinghn = hr[0] >= sr[0];
- boolean leadinghc = hr[0] < endshift;
- boolean trailinghc = hr[1] < endshift;
- if (leadinghn)
- {
- if (trailinghc)
- { // deleted hidden region.
- intervals.remove(i);
- pruned = true;
- j--;
- if (i <= j)
- {
- hr = intervals.get(i);
- }
- continue;
- }
- if (leadinghc)
- {
- hr[0] = endshift; // clip c terminal region
- leadinghn = !leadinghn;
- pruned = true;
- }
- }
- if (!leadinghn)
- {
- if (trailinghc)
- {
- if (trailinghn)
- {
- hr[1] = sr[0] - 1;
- pruned = true;
- }
- }
- else
- {
- // sr contained in hr
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- }
- }
- return pruned; // true if any interval was removed or modified by
- // operations.
- }
-
- /**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
- *
- * @param deletions
- */
- public void pruneDeletions(List<int[]> shifts)
- {
- try
- {
- LOCK.writeLock().lock();
- // delete any intervals intersecting.
- if (hiddenColumns != null)
- {
- pruneIntervalList(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
- *
- * @param profileseq
- * @param al
- * - alignment to have gaps inserted into it
- * @param input
- * - alignment view where sequence corresponding to profileseq is
- * first entry
- * @return new HiddenColumns for new alignment view, with insertions into
- * profileseq marked as hidden.
- */
- public static HiddenColumns propagateInsertions(SequenceI profileseq,
- AlignmentI al, AlignmentView input)
- {
- int profsqpos = 0;
-
- char gc = al.getGapCharacter();
- Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
- HiddenColumns nview = (HiddenColumns) alandhidden[1];
- SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
- nview.propagateInsertions(profileseq, al, origseq);
- return nview;
- }
-
- /**
- *
- * @param profileseq
- * - sequence in al which corresponds to origseq
- * @param al
- * - alignment which is to have gaps inserted into it
- * @param origseq
- * - sequence corresponding to profileseq which defines gap map for
- * modifying al
- */
- private void propagateInsertions(SequenceI profileseq, AlignmentI al,
- SequenceI origseq)
- {
- char gc = al.getGapCharacter();
- // recover mapping between sequence's non-gap positions and positions
- // mapping to view.
- pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
- int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
- int spos = 0;
- int offset = 0;
-
- // add profile to visible contigs
- for (int v = 0; v < viscontigs.length; v += 2)
- {
- if (viscontigs[v] > spos)
- {
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj != profileseq)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- if (sq.length() <= spos + offset)
- {
- // pad sequence
- int diff = spos + offset - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = spos + offset - sq.length() - 1) > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- }
- }
- sq += sb.toString();
- }
- else
- {
- al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset)
- + sb.toString() + sq.substring(spos + offset));
- }
- }
- }
- // offset+=sb.length();
- }
- spos = viscontigs[v + 1] + 1;
- }
- if ((offset + spos) < profileseq.getLength())
- {
- // pad the final region with gaps.
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = profileseq.getLength() - spos
- - offset; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj == profileseq)
- {
- continue;
- }
- String sq = sqobj.getSequenceAsString();
- // pad sequence
- int diff = origseq.getLength() - sq.length();
- while (diff > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- diff = origseq.getLength() - sq.length();
- }
- }
- }
- }
-
- /**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
- *
- * @param deletions
- */
- private void pruneDeletions(ShiftList deletions)
- {
- if (deletions != null)
- {
- final List<int[]> shifts = deletions.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- pruneDeletions(shifts);
-
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
- }
- }
-
- /**
- * Adjust hidden column boundaries based on a series of column additions or
- * deletions in visible regions.
- *
- * @param shiftrecord
- * @return
- */
- private ShiftList compensateForEdits(ShiftList shiftrecord)
- {
- if (shiftrecord != null)
- {
- final List<int[]> shifts = shiftrecord.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
- {
- int[] sh = shifts.get(i);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
- }
- }
- return shiftrecord.getInverse();
- }
- return null;
- }
-
- /**
- * Returns a hashCode built from hidden column ranges
- */
- @Override
- public int hashCode()
- {
- try
- {
- LOCK.readLock().lock();
- int hashCode = 1;
- if (hiddenColumns != null)
- {
- for (int[] hidden : hiddenColumns)
- {
- hashCode = 31 * hashCode + hidden[0];
- hashCode = 31 * hashCode + hidden[1];
- }
- }
- return hashCode;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * Hide columns corresponding to the marked bits
- *
- * @param inserts
- * - columns map to bits starting from zero
- */
- public void hideMarkedBits(BitSet inserts)
- {
- try
- {
- LOCK.writeLock().lock();
- for (int firstSet = inserts
- .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
- .nextSetBit(lastSet))
- {
- lastSet = inserts.nextClearBit(firstSet);
- hideColumns(firstSet, lastSet - 1);
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- *
- * @param inserts
- * BitSet where hidden columns will be marked
- */
- public void markHiddenRegions(BitSet inserts)
- {
- try
- {
- LOCK.readLock().lock();
- if (hiddenColumns == null)
- {
- return;
- }
- for (int[] range : hiddenColumns)
- {
- inserts.set(range[0], range[1] + 1);
- }
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * Calculate the visible start and end index of an alignment.
- *
- * @param width
- * full alignment width
- * @return integer array where: int[0] = startIndex, and int[1] = endIndex
- */
- public int[] getVisibleStartAndEndIndex(int width)
- {
- try
- {
- LOCK.readLock().lock();
- int[] alignmentStartEnd = new int[] { 0, width - 1 };
- int startPos = alignmentStartEnd[0];
- int endPos = alignmentStartEnd[1];
-
- int[] lowestRange = new int[] { -1, -1 };
- int[] higestRange = new int[] { -1, -1 };
-
- if (hiddenColumns == null)
- {
- return new int[] { startPos, endPos };
- }
-
- for (int[] hiddenCol : hiddenColumns)
- {
- lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
- higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
- }
-
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
- {
- startPos = alignmentStartEnd[0];
- }
- else
- {
- startPos = lowestRange[1] + 1;
- }
-
- if (higestRange[0] == -1 && higestRange[1] == -1)
- {
- endPos = alignmentStartEnd[1];
- }
- else
- {
- endPos = higestRange[0] - 1;
- }
- return new int[] { startPos, endPos };
- } finally
- {
- LOCK.readLock().unlock();
- }
-
- }
-
- /**
- * Finds the hidden region (if any) which starts or ends at res
- *
- * @param res
- * visible residue position, unadjusted for hidden columns
- * @return region as [start,end] or null if no matching region is found
- */
- public int[] getRegionWithEdgeAtRes(int res)
- {
- try
- {
- LOCK.readLock().lock();
- int adjres = adjustForHiddenColumns(res);
-
- int[] reveal = null;
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
- {
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
- {
- reveal = region;
- break;
- }
- }
- }
- return reveal;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class HiddenColumnsCursor
+{
+ // absolute position of first hidden column
+ private int firstColumn;
+
+ private List<int[]> hiddenColumns = new ArrayList<>();
+
+ private HiddenCursorPosition cursorPos = new HiddenCursorPosition(0, 0);
+
+ protected HiddenColumnsCursor()
+ {
+
+ }
+
+ protected HiddenColumnsCursor(List<int[]> hiddenCols)
+ {
+ resetCursor(hiddenCols, 0, 0);
+ }
+
+ protected HiddenColumnsCursor(List<int[]> hiddenCols, int index,
+ int hiddencount)
+ {
+ resetCursor(hiddenCols, index, hiddencount);
+ }
+
+ /**
+ * Reset the cursor with a new hidden columns collection, where we know in
+ * advance the index and hidden columns count of a particular location.
+ *
+ * @param hiddenCols
+ * new hidden columns collection
+ * @param index
+ * cursor index to reset to
+ * @param hiddencount
+ * hidden columns count to reset to
+ */
+ private void resetCursor(List<int[]> hiddenCols, int index,
+ int hiddencount)
+ {
+ hiddenColumns = hiddenCols;
+ if (!hiddenCols.isEmpty())
+ {
+ firstColumn = hiddenColumns.get(0)[0];
+ cursorPos = new HiddenCursorPosition(index,
+ hiddencount);
+ }
+ }
+
+ /**
+ * Get the cursor pointing to the hidden region that column is within (if
+ * column is hidden) or which is to the right of column (if column is
+ * visible). If no hidden columns are to the right, returns a cursor pointing
+ * to an imaginary hidden region beyond the end of the hidden columns
+ * collection (this ensures the count of previous hidden columns is correct).
+ * If hidden columns is empty returns null.
+ *
+ * @param column
+ * index of column in visible or absolute coordinates
+ * @param useVisible
+ * true if column is in visible coordinates, false if absolute
+ * @return cursor pointing to hidden region containing the column (if hidden)
+ * or to the right of the column (if visible)
+ */
+ protected HiddenCursorPosition findRegionForColumn(int column,
+ boolean useVisible)
+ {
+ if (hiddenColumns.isEmpty())
+ {
+ return null;
+ }
+
+ // used to add in hiddenColumns offset when working with visible columns
+ int offset = (useVisible ? 1 : 0);
+
+ HiddenCursorPosition pos = cursorPos;
+ int index = pos.getRegionIndex();
+ int hiddenCount = pos.getHiddenSoFar();
+
+ if (column < firstColumn)
+ {
+ pos = new HiddenCursorPosition(0, 0);
+ }
+
+ // column is after current region
+ else if ((index < hiddenColumns.size())
+ && (hiddenColumns.get(index)[0] <= column
+ + offset * hiddenCount))
+ {
+ // iterate from where we are now, if we're lucky we'll be close by
+ // (but still better than iterating from 0)
+ // stop when we find the region *before* column
+ // i.e. the next region starts after column or if not, ends after column
+ pos = searchForward(pos, column, useVisible);
+ }
+
+ // column is before current region
+ else
+ {
+ pos = searchBackward(pos, column, useVisible);
+ }
+ cursorPos = pos;
+ return pos;
+ }
+
+ /**
+ * Search forwards through the hidden columns collection to find the hidden
+ * region immediately before a column
+ *
+ * @param pos
+ * current position
+ * @param column
+ * column to locate
+ * @param useVisible
+ * whether using visible or absolute coordinates
+ * @return position of region before column
+ */
+ private HiddenCursorPosition searchForward(HiddenCursorPosition pos,
+ int column, boolean useVisible)
+ {
+ HiddenCursorPosition p = pos;
+ if (useVisible)
+ {
+ while ((p.getRegionIndex() < hiddenColumns.size())
+ && hiddenColumns.get(p.getRegionIndex())[0] <= column
+ + p.getHiddenSoFar())
+ {
+ p = stepForward(p);
+ }
+ }
+ else
+ {
+ while ((p.getRegionIndex() < hiddenColumns.size())
+ && hiddenColumns.get(p.getRegionIndex())[1] < column)
+ {
+ p = stepForward(p);
+ }
+ }
+ return p;
+ }
+
+ /**
+ * Move to the next (rightwards) hidden region after a given cursor position
+ *
+ * @param p
+ * current position of cursor
+ * @return new position of cursor at next region
+ */
+ private HiddenCursorPosition stepForward(HiddenCursorPosition p)
+ {
+ int[] region = hiddenColumns.get(p.getRegionIndex());
+
+ // increment the index, and add this region's hidden columns to the hidden
+ // column count
+ return new HiddenCursorPosition(p.getRegionIndex() + 1,
+ p.getHiddenSoFar() + region[1] - region[0] + 1);
+ }
+
+ /**
+ * Search backwards through the hidden columns collection to find the hidden
+ * region immediately before (left of) a given column
+ *
+ * @param pos
+ * current position
+ * @param column
+ * column to locate
+ * @param useVisible
+ * whether using visible or absolute coordinates
+ * @return position of region immediately to left of column
+ */
+ private HiddenCursorPosition searchBackward(HiddenCursorPosition p,
+ int column, boolean useVisible)
+ {
+ int i = p.getRegionIndex();
+ int h = p.getHiddenSoFar();
+
+ // used to add in hiddenColumns offset when working with visible columns
+ int offset = (useVisible ? 1 : 0);
+
+ while ((i > 0) && (hiddenColumns.get(i - 1)[1] >= column + offset * h))
+ {
+ i--;
+ int[] region = hiddenColumns.get(i);
+ h -= region[1] - region[0] + 1;
+ }
+ return new HiddenCursorPosition(i, h);
+ }
+
+}
--- /dev/null
+package jalview.datamodel;
+
+public final class HiddenCursorPosition
+{
+ // index of last visited region
+ private final int regionIndex;
+
+ // number of hidden columns before last visited region
+ private final int hiddenSoFar;
+
+ public HiddenCursorPosition(int index, int hiddencount)
+ {
+ regionIndex = index;
+ hiddenSoFar = hiddencount;
+ }
+
+ public int getRegionIndex()
+ {
+ return regionIndex;
+ }
+
+ public int getHiddenSoFar()
+ {
+ return hiddenSoFar;
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Data structure which stores a hidden Markov model
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HiddenMarkovModel
+{
+ private static final char GAP_DASH = '-';
+
+ public final static String YES = "yes";
+
+ public final static String NO = "no";
+
+ public static final int MATCHTOMATCH = 0;
+
+ public static final int MATCHTOINSERT = 1;
+
+ public static final int MATCHTODELETE = 2;
+
+ public static final int INSERTTOMATCH = 3;
+
+ public static final int INSERTTOINSERT = 4;
+
+ public static final int DELETETOMATCH = 5;
+
+ public static final int DELETETODELETE = 6;
+
+ private static final double LOG2 = Math.log(2);
+
+ /*
+ * properties read from HMM file header lines
+ */
+ private Map<String, String> fileProperties = new HashMap<>();
+
+ private String fileHeader;
+
+ /*
+ * the symbols used in this model e.g. "ACGT"
+ */
+ private String alphabet;
+
+ /*
+ * symbol lookup index into the alphabet for 'A' to 'Z'
+ */
+ private int[] symbolIndexLookup = new int['Z' - 'A' + 1];
+
+ /*
+ * Nodes in the model. The begin node is at index 0, and contains
+ * average emission probabilities for each symbol.
+ */
+ private List<HMMNode> nodes = new ArrayList<>();
+
+ /*
+ * the aligned HMM consensus sequence extracted from the HMM profile
+ */
+ private SequenceI hmmSeq;
+
+ /*
+ * mapping from HMM nodes to residues of the hmm consensus sequence
+ */
+ private Mapping mapToHmmConsensus;
+
+ /**
+ * Constructor
+ */
+ public HiddenMarkovModel()
+ {
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param hmm
+ */
+ public HiddenMarkovModel(HiddenMarkovModel hmm)
+ {
+ super();
+ this.fileProperties = new HashMap<>(hmm.fileProperties);
+ this.alphabet = hmm.alphabet;
+ this.nodes = new ArrayList<>(hmm.nodes);
+ this.symbolIndexLookup = hmm.symbolIndexLookup;
+ this.fileHeader = new String(hmm.fileHeader);
+ }
+
+ /**
+ * Returns the information content at a specified column, calculated as the
+ * sum (over possible symbols) of the log ratio
+ *
+ * <pre>
+ * log(emission probability / background probability) / log(2)
+ * </pre>
+ *
+ * @param column
+ * column position (base 0)
+ * @return
+ */
+ public float getInformationContent(int column)
+ {
+ float informationContent = 0f;
+
+ for (char symbol : getSymbols().toCharArray())
+ {
+ float freq = ResidueProperties.backgroundFrequencies
+ .get(getAlphabetType()).get(symbol);
+ float prob = (float) getMatchEmissionProbability(column, symbol);
+ informationContent += prob * Math.log(prob / freq);
+ }
+
+ informationContent = informationContent / (float) LOG2;
+
+ return informationContent;
+ }
+
+ /**
+ * Gets the file header of the .hmm file this model came from
+ *
+ * @return
+ */
+ public String getFileHeader()
+ {
+ return fileHeader;
+ }
+
+ /**
+ * Sets the file header of this model.
+ *
+ * @param header
+ */
+ public void setFileHeader(String header)
+ {
+ fileHeader = header;
+ }
+
+ /**
+ * Returns the symbols used in this hidden Markov model
+ *
+ * @return
+ */
+ public String getSymbols()
+ {
+ return alphabet;
+ }
+
+ /**
+ * Gets the node in the hidden Markov model at the specified position.
+ *
+ * @param nodeIndex
+ * The index of the node requested. Node 0 optionally contains the
+ * average match emission probabilities across the entire model, and
+ * always contains the insert emission probabilities and state
+ * transition probabilities for the begin node. Node 1 contains the
+ * first node in the HMM that can correspond to a column in the
+ * alignment.
+ * @return
+ */
+ public HMMNode getNode(int nodeIndex)
+ {
+ return nodes.get(nodeIndex);
+ }
+
+ /**
+ * Returns the name of the sequence alignment on which the HMM is based.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return fileProperties.get(HMMFile.NAME);
+ }
+
+ /**
+ * Answers the string value of the property (parsed from an HMM file) for the
+ * given key, or null if the property is not present
+ *
+ * @param key
+ * @return
+ */
+ public String getProperty(String key)
+ {
+ return fileProperties.get(key);
+ }
+
+ /**
+ * Answers true if the property with the given key is present with a value of
+ * "yes" (not case-sensitive), else false
+ *
+ * @param key
+ * @return
+ */
+ public boolean getBooleanProperty(String key)
+ {
+ return YES.equalsIgnoreCase(fileProperties.get(key));
+ }
+
+ /**
+ * Returns the length of the hidden Markov model. The value returned is the
+ * LENG property if specified, else the number of nodes, excluding the begin
+ * node (which should be the same thing).
+ *
+ * @return
+ */
+ public int getLength()
+ {
+ if (fileProperties.get(HMMFile.LENGTH) == null)
+ {
+ return nodes.size() - 1; // not counting BEGIN node
+ }
+ return Integer.parseInt(fileProperties.get(HMMFile.LENGTH));
+ }
+
+ /**
+ * Returns the value of mandatory property "ALPH" - "amino", "DNA", "RNA" are
+ * the options. Other alphabets may be added.
+ *
+ * @return
+ */
+ public String getAlphabetType()
+ {
+ return fileProperties.get(HMMFile.ALPHABET);
+ }
+
+ /**
+ * Sets the model alphabet to the symbols in the given string (ignoring any
+ * whitespace), and returns the number of symbols
+ *
+ * @param symbols
+ */
+ public int setAlphabet(String symbols)
+ {
+ String trimmed = symbols.toUpperCase().replaceAll("\\s", "");
+ int count = trimmed.length();
+ alphabet = trimmed;
+ symbolIndexLookup = new int['Z' - 'A' + 1];
+ Arrays.fill(symbolIndexLookup, -1);
+ int ignored = 0;
+
+ /*
+ * save the symbols in order, and a quick lookup of symbol position
+ */
+ for (short i = 0; i < count; i++)
+ {
+ char symbol = trimmed.charAt(i);
+ if (symbol >= 'A' && symbol <= 'Z'
+ && symbolIndexLookup[symbol - 'A'] == -1)
+ {
+ symbolIndexLookup[symbol - 'A'] = i;
+ }
+ else
+ {
+ System.err
+ .println(
+ "Unexpected or duplicated character in HMM ALPHabet: "
+ + symbol);
+ ignored++;
+ }
+ }
+ return count - ignored;
+ }
+
+ /**
+ * Answers the node of the model corresponding to an aligned column position
+ * (0...), or null if there is no such node
+ *
+ * @param column
+ * @return
+ */
+ HMMNode getNodeForColumn(int column)
+ {
+ /*
+ * if the hmm consensus is gapped at the column,
+ * there is no corresponding node
+ */
+ if (Comparison.isGap(hmmSeq.getCharAt(column)))
+ {
+ return null;
+ }
+
+ /*
+ * find the node (if any) that is mapped to the
+ * consensus sequence residue position at the column
+ */
+ int seqPos = hmmSeq.findPosition(column);
+ int[] nodeNo = mapToHmmConsensus.getMap().locateInFrom(seqPos, seqPos);
+ if (nodeNo != null)
+ {
+ return getNode(nodeNo[0]);
+ }
+ return null;
+ }
+
+ /**
+ * Gets the match emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public double getMatchEmissionProbability(int alignColumn, char symbol)
+ {
+ HMMNode node = getNodeForColumn(alignColumn);
+ int symbolIndex = getSymbolIndex(symbol);
+ if (node != null && symbolIndex != -1)
+ {
+ return node.getMatchEmission(symbolIndex);
+ }
+ return 0D;
+ }
+
+ /**
+ * Gets the insert emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public double getInsertEmissionProbability(int alignColumn, char symbol)
+ {
+ HMMNode node = getNodeForColumn(alignColumn);
+ int symbolIndex = getSymbolIndex(symbol);
+ if (node != null && symbolIndex != -1)
+ {
+ return node.getInsertEmission(symbolIndex);
+ }
+ return 0D;
+ }
+
+ /**
+ * Gets the state transition probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public double getStateTransitionProbability(int alignColumn,
+ int transition)
+ {
+ HMMNode node = getNodeForColumn(alignColumn);
+ if (node != null)
+ {
+ return node.getStateTransition(transition);
+ }
+ return 0D;
+ }
+
+ /**
+ * Returns the sequence position linked to the node at the given index. This
+ * corresponds to an aligned column position (counting from 1).
+ *
+ * @param nodeIndex
+ * The index of the node, starting from index 1. Index 0 is the begin
+ * node, which does not correspond to a column in the alignment.
+ * @return
+ */
+ public int getNodeMapPosition(int nodeIndex)
+ {
+ return nodes.get(nodeIndex).getResidueNumber();
+ }
+
+ /**
+ * Returns the consensus residue at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusResidue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusResidue();
+ return value;
+ }
+
+ /**
+ * Returns the reference annotation at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getReferenceAnnotation(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getReferenceAnnotation();
+ return value;
+ }
+
+ /**
+ * Returns the mask value at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getMaskedValue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getMaskValue();
+ return value;
+ }
+
+ /**
+ * Returns the consensus structure at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusStructure(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusStructure();
+ return value;
+ }
+
+ /**
+ * Sets a property read from an HMM file
+ *
+ * @param key
+ * @param value
+ */
+ public void setProperty(String key, String value)
+ {
+ fileProperties.put(key, value);
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getViterbi()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.VITERBI);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getMSV()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.MSV);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getForward()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.FORWARD);
+ return value;
+ }
+
+ /**
+ * Constructs the consensus sequence based on the most probable symbol at each
+ * position. Gap characters are inserted for discontinuities in the node map
+ * numbering (if provided), else an ungapped sequence is generated.
+ * <p>
+ * A mapping between the HMM nodes and residue positions of the sequence is
+ * also built and saved.
+ *
+ * @return
+ */
+ void buildConsensusSequence()
+ {
+ List<int[]> toResidues = new ArrayList<>();
+
+ /*
+ * if the HMM provided a map to sequence, use those start/end values,
+ * else just treat it as for a contiguous sequence numbered from 1
+ */
+ boolean hasMap = getBooleanProperty(HMMFile.MAP);
+ int start = hasMap ? getNode(1).getResidueNumber() : 1;
+ int endResNo = hasMap ? getNode(nodes.size() - 1).getResidueNumber()
+ : (start + getLength() - 1);
+ char[] sequence = new char[endResNo - start + 1];
+
+ int lastResNo = start - 1;
+ int seqOffset = 0;
+ int gapCount = 0;
+
+ for (int nodeNo = 1; nodeNo < nodes.size(); nodeNo++)
+ {
+ HMMNode node = nodes.get(nodeNo);
+ final int resNo = hasMap ? node.getResidueNumber() : lastResNo + 1;
+
+ /*
+ * insert gaps if map numbering is not continuous
+ */
+ while (resNo > lastResNo + 1)
+ {
+ sequence[seqOffset++] = '-';
+ lastResNo++;
+ gapCount++;
+ }
+ char consensusResidue = node.getConsensusResidue();
+ if (GAP_DASH == consensusResidue)
+ {
+ /*
+ * no residue annotation in HMM - scan for the symbol
+ * with the highest match emission probability
+ */
+ int symbolIndex = node.getMaxMatchEmissionIndex();
+ consensusResidue = alphabet.charAt(symbolIndex);
+ if (node.getMatchEmission(symbolIndex) < 0.5D)
+ {
+ // follow convention of lower case if match emission prob < 0.5
+ consensusResidue = Character.toLowerCase(consensusResidue);
+ }
+ }
+ sequence[seqOffset++] = consensusResidue;
+ lastResNo = resNo;
+ }
+
+ Sequence seq = new Sequence(getName(), sequence, start,
+ lastResNo - gapCount);
+ seq.createDatasetSequence();
+ seq.setHMM(this);
+ seq.setIsHMMConsensusSequence(true);
+
+ this.hmmSeq = seq;
+
+ /*
+ * construct and store Mapping of nodes to residues
+ * note as constructed this is just an identity mapping,
+ * but it allows for greater flexibility in future
+ */
+ List<int[]> fromNodes = new ArrayList<>();
+ fromNodes.add(new int[] { 1, getLength() });
+ toResidues.add(new int[] { seq.getStart(), seq.getEnd() });
+ MapList mapList = new MapList(fromNodes, toResidues, 1, 1);
+ mapToHmmConsensus = new Mapping(seq.getDatasetSequence(), mapList);
+ }
+
+
+ /**
+ * Answers the aligned consensus sequence for the profile. Note this will
+ * return null if called before <code>setNodes</code> has been called.
+ *
+ * @return
+ */
+ public SequenceI getConsensusSequence()
+ {
+ return hmmSeq;
+ }
+
+ /**
+ * Answers the index position (0...) of the given symbol, or -1 if not a valid
+ * symbol for this HMM
+ *
+ * @param symbol
+ * @return
+ */
+ private int getSymbolIndex(char symbol)
+ {
+ /*
+ * symbolIndexLookup holds the index for 'A' to 'Z'
+ */
+ char c = Character.toUpperCase(symbol);
+ if ('A' <= c && c <= 'Z')
+ {
+ return symbolIndexLookup[c - 'A'];
+ }
+ return -1;
+ }
+
+ /**
+ * Sets the nodes of this HMM, and also extracts the HMM consensus sequence
+ * and a mapping between node numbers and sequence positions
+ *
+ * @param nodeList
+ */
+ public void setNodes(List<HMMNode> nodeList)
+ {
+ nodes = nodeList;
+ buildConsensusSequence();
+ }
+}
+
--- /dev/null
+package jalview.datamodel;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+/**
+ * Iterator over each element in a set of ranges i.e. if ranges is {[3,6],
+ * [12,15]} it will iterate over {3,4,5,6,12,13,14,15}. Uses a local copy of the
+ * set of ranges.
+ *
+ * @author kmourao
+ *
+ */
+public class RangeElementsIterator implements Iterator<Integer>
+{
+ private int last;
+
+ private int current;
+
+ private int next;
+
+ private Iterator<int[]> rangeIterator;
+
+ private int[] nextRange = null;
+
+ RangeElementsIterator(Iterator<int[]> it)
+ {
+ rangeIterator = it;
+ if (rangeIterator.hasNext())
+ {
+ nextRange = rangeIterator.next();
+ next = nextRange[0];
+ last = nextRange[1];
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return rangeIterator.hasNext() || next <= last;
+ }
+
+ @Override
+ public Integer next()
+ {
+ if (!hasNext())
+ {
+ throw new NoSuchElementException();
+ }
+
+ current = next;
+
+ // recalculate next
+ next++;
+
+ // if there are more ranges need to check if next is in a range
+ checkNextRange();
+ return current;
+ }
+
+ /**
+ * Check how next position relates to next range, and update next position if
+ * necessary
+ */
+ private void checkNextRange()
+ {
+ if (nextRange != null && next > nextRange[1])
+ {
+ if (rangeIterator.hasNext())
+ {
+ nextRange = rangeIterator.next();
+ next = nextRange[0];
+ last = nextRange[1];
+ }
+ else
+ {
+ nextRange = null;
+ }
+
+ }
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over a list of ranges. Works with a copy of the
+ * collection of ranges.
+ */
+public class RangeIterator implements Iterator<int[]>
+{
+ // current index in rangeList
+ private int currentPosition = 0;
+
+ // current range in rangeList
+ private int[] currentRange;
+
+ // local copy or reference to rangeList
+ private List<int[]> localRanges;
+
+ /**
+ * Unbounded constructor
+ *
+ * @param rangeList
+ * list of ranges to iterate over
+ */
+ RangeIterator(List<int[]> rangeList)
+ {
+ if (!rangeList.isEmpty())
+ {
+ int last = rangeList.get(rangeList.size() - 1)[1];
+ init(0, last, rangeList);
+ }
+ else
+ {
+ init(0, 0, rangeList);
+ }
+ }
+
+ /**
+ * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate from
+ * @param upperBound
+ * upper bound to iterate to
+ * @param rangeList
+ * list of ranges to iterate over
+ */
+ RangeIterator(int lowerBound, int upperBound,
+ List<int[]> rangeList)
+ {
+ init(lowerBound, upperBound, rangeList);
+ }
+
+ /**
+ * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate from
+ * @param upperBound
+ * upper bound to iterate to
+ */
+ private void init(int lowerBound, int upperBound,
+ List<int[]> rangeList)
+ {
+ int start = lowerBound;
+ int end = upperBound;
+
+ if (rangeList != null)
+ {
+ localRanges = new ArrayList<>();
+
+ // iterate until a range overlaps with [start,end]
+ int i = 0;
+ while ((i < rangeList.size()) && (rangeList.get(i)[1] < start))
+ {
+ i++;
+ }
+
+ // iterate from start to end, adding each range. Positions are
+ // absolute, and all ranges which *overlap* [start,end] are added.
+ while (i < rangeList.size() && (rangeList.get(i)[0] <= end))
+ {
+ int[] rh = rangeList.get(i);
+ int[] cp = new int[2];
+ System.arraycopy(rh, 0, cp, 0, rh.length);
+ localRanges.add(cp);
+ i++;
+ }
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (localRanges != null) && (currentPosition < localRanges.size());
+ }
+
+ @Override
+ public int[] next()
+ {
+ currentRange = localRanges.get(currentPosition);
+ currentPosition++;
+ return currentRange;
+ }
+
+ @Override
+ public void remove()
+ {
+ localRanges.remove(--currentPosition);
+ }
+}
import jalview.util.QuickSort;
import jalview.util.SparseCount;
+import java.util.List;
+
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
}
/**
+ * A constructor that counts frequency of all symbols (including gaps) in the
+ * sequences (not case-sensitive)
+ *
+ * @param sequences
+ */
+ public ResidueCount(List<SequenceI> sequences)
+ {
+ this();
+ for (SequenceI seq : sequences)
+ {
+ for (int i = 0; i < seq.getLength(); i++)
+ {
+ add(seq.getCharAt(i));
+ }
+ }
+ }
+
+ /**
* Increments the count for the given character. The supplied character may be
* upper or lower case but counts are for the upper case only. Gap characters
* (space, ., -) are all counted together.
sb.append("]");
return sb.toString();
}
+
+ /**
+ * Answers the total count for all symbols (excluding gaps)
+ *
+ * @return
+ */
+ public int getTotalResidueCount()
+ {
+ int total = 0;
+ for (char symbol : this.getSymbolCounts().symbols)
+ {
+ total += getCount(symbol);
+ }
+ return total;
+ }
}
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
+import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
import java.util.Vector;
int end;
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
+
Vector<PDBEntry> pdbIds;
String vamsasId;
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.isHMMConsensusSequence())
+ {
+ this.isHMMConsensusSequence = true;
+ }
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM());
+ }
+
}
@Override
{
if (pdbIds == null)
{
- pdbIds = new Vector<PDBEntry>();
+ pdbIds = new Vector<>();
pdbIds.add(entry);
return true;
}
@Override
public Vector<PDBEntry> getAllPDBEntries()
{
- return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+ return pdbIds == null ? new Vector<>() : pdbIds;
}
/**
return map;
}
+ /**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ @Override
+ public BitSet gapBitset()
+ {
+ BitSet gaps = new BitSet(sequence.length);
+ int j = 0;
+ while (j < sequence.length)
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ gaps.set(j);
+ }
+ j++;
+ }
+ return gaps;
+ }
+
@Override
public int[] findPositionMap()
{
@Override
public List<int[]> getInsertions()
{
- ArrayList<int[]> map = new ArrayList<int[]>();
+ ArrayList<int[]> map = new ArrayList<>();
int lastj = -1, j = 0;
int pos = start;
int seqlen = sequence.length;
{
if (this.annotation == null)
{
- this.annotation = new Vector<AlignmentAnnotation>();
+ this.annotation = new Vector<>();
}
if (!this.annotation.contains(annotation))
{
return null;
}
- Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> subset = new Vector<>();
Enumeration<AlignmentAnnotation> e = annotation.elements();
while (e.hasMoreElements())
{
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
- List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
+ String id = ann.getCalcId();
+ if (id != null && id.equals(calcId)
&& ann.label != null && ann.label.equals(label))
{
result.add(ann);
}
synchronized (dbrefs)
{
- List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> primaries = new ArrayList<>();
DBRefEntry[] tmp = new DBRefEntry[1];
for (DBRefEntry ref : dbrefs)
{
}
}
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public boolean isHMMConsensusSequence()
+ {
+ return isHMMConsensusSequence;
+ }
+
+ @Override
+ public void setIsHMMConsensusSequence(boolean value)
+ {
+ this.isHMMConsensusSequence = value;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ if (this.annotation == null) {
+ return false;
+ }
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
/**
* {@inheritDoc}
*/
return count;
}
+
+ @Override
+ public String getSequenceStringFromIterator(Iterator<int[]> it)
+ {
+ StringBuilder newSequence = new StringBuilder();
+ while (it.hasNext())
+ {
+ int[] block = it.next();
+ if (it.hasNext())
+ {
+ newSequence.append(getSequence(block[0], block[1] + 1));
+ }
+ else
+ {
+ newSequence.append(getSequence(block[0], block[1]));
+ }
+ }
+
+ return newSequence.toString();
+ }
+
+ @Override
+ public int firstResidueOutsideIterator(Iterator<int[]> regions)
+ {
+ int start = 0;
+
+ if (!regions.hasNext())
+ {
+ return findIndex(getStart()) - 1;
+ }
+
+ // Simply walk along the sequence whilst watching for region
+ // boundaries
+ int hideStart = getLength();
+ int hideEnd = -1;
+ boolean foundStart = false;
+
+ // step through the non-gapped positions of the sequence
+ for (int i = getStart(); i <= getEnd() && (!foundStart); i++)
+ {
+ // get alignment position of this residue in the sequence
+ int p = findIndex(i) - 1;
+
+ // update region start/end
+ while (hideEnd < p && regions.hasNext())
+ {
+ int[] region = regions.next();
+ hideStart = region[0];
+ hideEnd = region[1];
+ }
+ if (hideEnd < p)
+ {
+ hideStart = getLength();
+ }
+ // update boundary for sequence
+ if (p < hideStart)
+ {
+ start = p;
+ foundStart = true;
+ }
+ }
+
+ if (foundStart)
+ {
+ return start;
+ }
+ // otherwise, sequence was completely hidden
+ return 0;
+ }
}
* @return
*/
boolean isNucleotide();
+
+ /**
+ * Returns the HMM consensus sequence (if any) for the collection, or null
+ *
+ * @return
+ */
+ SequenceI getHmmConsensus();
+
+ /**
+ * Sets the HMM consensus sequence for the collection
+ */
+ void setHmmConsensus(SequenceI hmmSeq);
}
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
import java.awt.Color;
import java.beans.PropertyChangeListener;
public class SequenceGroup implements AnnotatedCollectionI
{
// TODO ideally this event notification functionality should be separated into
- // a
- // subclass of ViewportProperties similarly to ViewportRanges. Done here as
- // quick fix for JAL-2665
+ // a subclass of ViewportProperties similarly to ViewportRanges.
+ // Done here as a quick fix for JAL-2665
public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
+ private String groupName;
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
+ private String description;
- public void removePropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
- // end of event notification functionality initialisation
+ private AnnotatedCollectionI context;
- String groupName;
+ private Conservation conservationData;
- String description;
+ private ProfilesI consensusProfiles;
- Conservation conserve;
+ private ProfilesI hmmProfiles;
- boolean displayBoxes = true;
+ private boolean displayBoxes = true;
- boolean displayText = true;
+ private boolean displayText = true;
- boolean colourText = false;
+ private boolean colourText = false;
- /**
- * True if the group is defined as a group on the alignment, false if it is
- * just a selection.
+ /*
+ * true if the group is defined as a group on the alignment, false if it is
+ * just a selection
*/
- boolean isDefined = false;
+ private boolean isDefined;
- /**
+ /*
* after Olivier's non-conserved only character display
*/
- boolean showNonconserved = false;
+ private boolean showNonconserved;
- /**
- * group members
+ /*
+ * sequences in the group
*/
private List<SequenceI> sequences = new ArrayList<>();
- /**
+ /*
* representative sequence for this group (if any)
*/
- private SequenceI seqrep = null;
+ private SequenceI seqrep;
+
+ /*
+ * HMM consensus sequence for group (if any)
+ */
+ private SequenceI hmmConsensus;
- int width = -1;
+ private int width = -1;
- /**
- * Colourscheme applied to group if any
+ /*
+ * colour scheme applied to group if any
*/
public ResidueShaderI cs;
// start column (base 0)
- int startRes = 0;
+ private int startRes;
// end column (base 0)
- int endRes = 0;
+ private int endRes;
public Color outlineColour = Color.black;
- public Color idColour = null;
+ public Color idColour;
- public int thresholdTextColour = 0;
+ public int thresholdTextColour;
public Color textColour = Color.black;
public Color textColour2 = Color.white;
- /**
- * consensus calculation property
+ /*
+ * properties for consensus annotation
*/
private boolean ignoreGapsInConsensus = true;
- /**
- * consensus calculation property
- */
- private boolean showSequenceLogo = false;
+ private boolean showSequenceLogo;
- /**
- * flag indicating if logo should be rendered normalised
- */
private boolean normaliseSequenceLogo;
+ private boolean showConsensusHistogram;
+
+ /*
+ * properties for HMM information annotation
+ */
+ private boolean hmmIgnoreBelowBackground = true;
+
+ private boolean hmmUseInfoLetterHeight;
+
+ private boolean hmmShowSequenceLogo;
+
+ private boolean hmmNormaliseSequenceLogo;
+
+ private boolean hmmShowHistogram;
+
/*
* visibility of rows or represented rows covered by group
*/
- private boolean hidereps = false;
+ private boolean hidereps;
/*
* visibility of columns intersecting this group
*/
- private boolean hidecols = false;
-
- AlignmentAnnotation consensus = null;
+ private boolean hidecols;
- AlignmentAnnotation conservation = null;
+ private AlignmentAnnotation consensus;
- private boolean showConsensusHistogram;
+ private AlignmentAnnotation conservation;
- private AnnotatedCollectionI context;
+ private AlignmentAnnotation hmmInformation;
/**
- * Creates a new SequenceGroup object.
+ * Constructor, assigning a generated default name of "JGroup:" with object
+ * hashcode appended
*/
public SequenceGroup()
{
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
+ hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
+ hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
+ hmmShowHistogram = seqsel.hmmShowHistogram;
idColour = seqsel.idColour;
outlineColour = seqsel.outlineColour;
seqrep = seqsel.seqrep;
thresholdTextColour = seqsel.thresholdTextColour;
width = seqsel.width;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
- if (seqsel.conserve != null)
+ hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
+ hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
+ if (seqsel.conservationData != null)
{
recalcConservation(); // safer than
// aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
}
}
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
seqs[ipos].setDescription(seq.getDescription());
seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
*/
public Conservation getConservation()
{
- return conserve;
+ return conservationData;
}
/**
*/
public void setConservation(Conservation c)
{
- conserve = c;
+ conservationData = c;
}
/**
*/
public boolean recalcConservation()
{
- return recalcConservation(false);
+ return recalcAnnotations(false);
}
/**
- * calculate residue conservation for group - but only if necessary. returns
- * true if the calculation resulted in a visible change to group
+ * Recalculates column consensus, conservation, and HMM annotation for the
+ * group (as applicable). Returns true if the calculation resulted in a
+ * visible change to group.
*
* @param defer
* when set, colourschemes for this group are not refreshed after
* recalculation
*/
- public boolean recalcConservation(boolean defer)
+ public boolean recalcAnnotations(boolean defer)
{
- if (cs == null && consensus == null && conservation == null)
+ if (cs == null && consensus == null && conservation == null
+ && hmmInformation == null)
{
return false;
}
{
ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
+ if (hmmInformation != null)
+ {
+ HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM();
+
+ ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+ (endRes + 1) - startRes, startRes, endRes + 1,
+ hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+ _updateInformationRow(info);
+ upd = true;
+ }
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
- public ProfilesI consensusData = null;
-
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
}
consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
- consensusData = cnsns;
+ consensusProfiles = cnsns;
// preserve width if already set
int aWidth = (consensus.annotations != null)
? (endRes < consensus.annotations.length
}
/**
+ * Recalculates the information content on the HMM annotation
+ *
+ * @param cnsns
+ */
+ private void _updateInformationRow(ProfilesI cnsns)
+ {
+ if (hmmInformation == null)
+ {
+ createInformationAnnotation();
+ }
+ hmmInformation.description = MessageManager
+ .getString("label.information_description");
+ setHmmProfiles(cnsns);
+ // preserve width if already set
+ int aWidth = (hmmInformation.annotations != null)
+ ? (endRes < hmmInformation.annotations.length
+ ? hmmInformation.annotations.length : endRes + 1)
+ : endRes + 1;
+ hmmInformation.annotations = null;
+ hmmInformation.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+ hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+ AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+ endRes + 1);
+ }
+
+ /**
* @param s
* sequence to either add or remove from group
* @param recalc
}
/**
+ * Creates the Hidden Markov Model annotation for this group
+ */
+ void createInformationAnnotation()
+ {
+ hmmInformation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 6.25f, AlignmentAnnotation.BAR_GRAPH);
+ hmmInformation.hasText = true;
+ hmmInformation.autoCalculated = false;
+ hmmInformation.groupRef = this;
+ hmmInformation.label = getName();
+ hmmInformation.description = MessageManager
+ .getString("label.information_description");
+ hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+ }
+
+ /**
* set this alignmentAnnotation object as the one used to render consensus
* annotation
*
{
if (consensus.annotations[i] != null)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String desc = consensus.annotations[i].description;
+ if (desc.length() > 1 && desc.charAt(0) == '[')
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ seqs.append(desc.charAt(1));
}
else
{
ignoreGapsInConsensus = state;
}
- public boolean getIgnoreGapsConsensus()
+ public boolean isIgnoreGapsConsensus()
{
return ignoreGapsInConsensus;
}
+ public void setIgnoreBelowBackground(boolean state)
+ {
+ hmmIgnoreBelowBackground = state;
+ }
+
+ public boolean isIgnoreBelowBackground()
+ {
+ return hmmIgnoreBelowBackground;
+ }
+
+ public void setInfoLetterHeight(boolean state)
+ {
+ hmmUseInfoLetterHeight = state;
+ }
+
+ public boolean isUseInfoLetterHeight()
+ {
+ return hmmUseInfoLetterHeight;
+ }
+
/**
* @param showSequenceLogo
* indicates if a sequence logo is shown for consensus annotation
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ public boolean isShowInformationHistogram()
+ {
+ return hmmShowHistogram;
+ }
+
+ public void setShowInformationHistogram(boolean state)
+ {
+ if (hmmShowHistogram != state && hmmInformation != null)
+ {
+ this.hmmShowHistogram = state;
+ // recalcConservation(); TODO don't know what to do here next
+ }
+ this.hmmShowHistogram = state;
+ }
+
+ public boolean isShowHMMSequenceLogo()
+ {
+ return hmmShowSequenceLogo;
+ }
+
+ public void setShowHMMSequenceLogo(boolean state)
+ {
+ hmmShowSequenceLogo = state;
+ }
+
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return hmmNormaliseSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ hmmNormaliseSequenceLogo = state;
+ }
+
+ @Override
+ public SequenceI getHmmConsensus()
+ {
+ return hmmConsensus;
+ }
+
+ @Override
+ public void setHmmConsensus(SequenceI hmmSeq)
+ {
+ this.hmmConsensus = hmmSeq;
+ }
+
+ public ProfilesI getConsensusData()
+ {
+ return consensusProfiles;
+ }
+
+ public ProfilesI getHmmProfiles()
+ {
+ return hmmProfiles;
+ }
+
+ public void setHmmProfiles(ProfilesI hmmProfiles)
+ {
+ this.hmmProfiles = hmmProfiles;
+ }
+
}
import jalview.util.MapList;
import java.util.BitSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Vector;
*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
+
/**
* Get the display name
*/
public int[] gapMap();
/**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ public BitSet gapBitset();
+
+ /**
* Returns an int array where indices correspond to each position in sequence
* char array and the element value gives the result of findPosition for that
* index in the sequence.
*/
public List<DBRefEntry> getPrimaryDBRefs();
+ boolean isHMMConsensusSequence();
+
+ void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+ /**
+ * Answers true if the sequence has annotation for Hidden Markov Model
+ * information content, else false
+ */
+ boolean hasHMMAnnotation();
+
/**
* Returns a (possibly empty) list of sequence features that overlap the given
* alignment column range, optionally restricted to one or more specified
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ int replace(char c1, char c2);
/**
* Answers the GeneLociI, or null if not known
*/
void setGeneLoci(String speciesId, String assemblyId,
String chromosomeId, MapList map);
+
+
+ /**
+ * Returns the sequence string constructed from the substrings of a sequence
+ * defined by the int[] ranges provided by an iterator. E.g. the iterator
+ * could iterate over all visible regions of the alignment
+ *
+ * @param it
+ * the iterator to use
+ * @return a String corresponding to the sequence
+ */
+ public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+ /**
+ * Locate the first position in this sequence which is not contained in an
+ * iterator region. If no such position exists, return 0
+ *
+ * @param it
+ * iterator over regions
+ * @return first residue not contained in regions
+ */
+ public int firstResidueOutsideIterator(Iterator<int[]> it);
}
--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over visible start positions of hidden column
+ * regions in a range.
+ */
+public class StartRegionIterator implements Iterator<Integer>
+{
+ // start position to iterate from
+ private int start;
+
+ // end position to iterate to
+ private int end;
+
+ // current index in hiddenColumns
+ private int currentPosition = 0;
+
+ // local copy or reference to hiddenColumns
+ private List<Integer> positions = null;
+
+ /**
+ * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate from
+ * @param upperBound
+ * upper bound to iterate to
+ * @param useCopyCols
+ * whether to make a local copy of hiddenColumns for iteration (set
+ * to true if calling from outwith the HiddenColumns class)
+ */
+ StartRegionIterator(int lowerBound, int upperBound,
+ List<int[]> hiddenColumns)
+ {
+ this(null, lowerBound, upperBound, hiddenColumns);
+ }
+
+ /**
+ * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
+ *
+ * @param pos
+ * a hidden cursor position to start from - may be null
+ * @param lowerBound
+ * lower bound to iterate from - will be ignored if pos != null
+ * @param upperBound
+ * upper bound to iterate to
+ * @param hiddenColumns
+ * the hidden columns collection to use
+ */
+ StartRegionIterator(HiddenCursorPosition pos, int lowerBound,
+ int upperBound, List<int[]> hiddenColumns)
+ {
+ start = lowerBound;
+ end = upperBound;
+
+ if (hiddenColumns != null)
+ {
+ positions = new ArrayList<>(hiddenColumns.size());
+
+ // navigate to start, keeping count of hidden columns
+ int i = 0;
+ int hiddenSoFar = 0;
+
+ if (pos != null)
+ {
+ // use the cursor position provided
+ i = pos.getRegionIndex();
+ hiddenSoFar = pos.getHiddenSoFar();
+ }
+ else
+ {
+ // navigate to start
+ while ((i < hiddenColumns.size())
+ && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
+ {
+ int[] region = hiddenColumns.get(i);
+ hiddenSoFar += region[1] - region[0] + 1;
+ i++;
+ }
+ }
+
+ // iterate from start to end, adding start positions of each
+ // hidden region. Positions are visible columns count, not absolute
+ while (i < hiddenColumns.size()
+ && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
+ {
+ int[] region = hiddenColumns.get(i);
+ positions.add(region[0] - hiddenSoFar);
+ hiddenSoFar += region[1] - region[0] + 1;
+ i++;
+ }
+ }
+ else
+ {
+ positions = new ArrayList<>();
+ }
+
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (currentPosition < positions.size());
+ }
+
+ /**
+ * Get next hidden region start position
+ *
+ * @return the start position in *visible* coordinates
+ */
+ @Override
+ public Integer next()
+ {
+ int result = positions.get(currentPosition);
+ currentPosition++;
+ return result;
+ }
+}
+
HiddenColumns hidden;
- public VisibleColsCollection(int s, int e, AlignmentI al)
+ public VisibleColsCollection(int s, int e, HiddenColumns h)
{
start = s;
end = e;
- hidden = al.getHiddenColumns();
+ hidden = h;
}
@Override
public Iterator<Integer> iterator()
{
- return new VisibleColsIterator(start, end, hidden);
+ return hidden.getVisibleColsIterator(start, end);
}
@Override
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel;
-
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-
-/**
- * An iterator which iterates over all visible columns in an alignment
- *
- * @author kmourao
- *
- */
-public class VisibleColsIterator implements Iterator<Integer>
-{
- private int last;
-
- private int current;
-
- private int next;
-
- private List<int[]> hidden;
-
- private int lasthiddenregion;
-
- public VisibleColsIterator(int firstcol, int lastcol,
- HiddenColumns hiddenCols)
- {
- last = lastcol;
- current = firstcol;
- next = firstcol;
- hidden = hiddenCols.getHiddenColumnsCopy();
- lasthiddenregion = -1;
-
- if (hidden != null)
- {
- int i = 0;
- for (i = 0; i < hidden.size(); ++i)
- {
- if (current >= hidden.get(i)[0] && current <= hidden.get(i)[1])
- {
- // current is hidden, move to right
- current = hidden.get(i)[1] + 1;
- next = current;
- }
- if (current < hidden.get(i)[0])
- {
- break;
- }
- }
- lasthiddenregion = i - 1;
-
- for (i = hidden.size() - 1; i >= 0; --i)
- {
- if (last >= hidden.get(i)[0] && last <= hidden.get(i)[1])
- {
- // last is hidden, move to left
- last = hidden.get(i)[0] - 1;
- }
- if (last > hidden.get(i)[1])
- {
- break;
- }
- }
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return next <= last;
- }
-
- @Override
- public Integer next()
- {
- if (next > last)
- {
- throw new NoSuchElementException();
- }
- current = next;
- if ((hidden != null) && (lasthiddenregion + 1 < hidden.size()))
- {
- // still some more hidden regions
- if (next + 1 < hidden.get(lasthiddenregion + 1)[0])
- {
- // next+1 is still before the next hidden region
- next++;
- }
- else if ((next + 1 >= hidden.get(lasthiddenregion + 1)[0])
- && (next + 1 <= hidden.get(lasthiddenregion + 1)[1]))
- {
- // next + 1 is in the next hidden region
- next = hidden.get(lasthiddenregion + 1)[1] + 1;
- lasthiddenregion++;
- }
- }
- else
- {
- // finished with hidden regions, just increment normally
- next++;
- }
- return current;
- }
-
- @Override
- public void remove()
- {
- throw new UnsupportedOperationException();
- }
-}
--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over visible regions in a range. Provides a
+ * special "endsAtHidden" indicator to allow callers to determine if the final
+ * visible column is adjacent to a hidden region.
+ */
+public class VisibleContigsIterator implements Iterator<int[]>
+{
+ private List<int[]> vcontigs = new ArrayList<>();
+
+ private int currentPosition = 0;
+
+ private boolean endsAtHidden = false;
+
+ VisibleContigsIterator(int start, int end,
+ List<int[]> hiddenColumns)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ int vstart = start;
+ int hideStart;
+ int hideEnd;
+
+ for (int[] region : hiddenColumns)
+ {
+ endsAtHidden = false;
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ // navigate to start
+ if (hideEnd < vstart)
+ {
+ continue;
+ }
+ if (hideStart > vstart)
+ {
+ if (end - 1 > hideStart - 1)
+ {
+ int[] contig = new int[] { vstart, hideStart - 1 };
+ vcontigs.add(contig);
+ endsAtHidden = true;
+ }
+ else
+ {
+ int[] contig = new int[] { vstart, end - 1 };
+ vcontigs.add(contig);
+ }
+ }
+ vstart = hideEnd + 1;
+
+ // exit if we're past the end
+ if (vstart >= end)
+ {
+ break;
+ }
+ }
+
+ if (vstart < end)
+ {
+ int[] contig = new int[] { vstart, end - 1 };
+ vcontigs.add(contig);
+ endsAtHidden = false;
+ }
+ }
+ else
+ {
+ int[] contig = new int[] { start, end - 1 };
+ vcontigs.add(contig);
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (currentPosition < vcontigs.size());
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] result = vcontigs.get(currentPosition);
+ currentPosition++;
+ return result;
+ }
+
+ public boolean endsAtHidden()
+ {
+ return endsAtHidden;
+ }
+}
+
*/
package jalview.ext.ensembl;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+
/**
* A class to behave much like EnsemblGene but referencing the ensemblgenomes
* domain and data
*/
public EnsemblGenomes()
{
- super(ENSEMBL_GENOMES_REST);
+ super();
+ setDomain(Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+ DEFAULT_ENSEMBL_GENOMES_BASEURL));
}
@Override
public String getDbName()
{
- return "EnsemblGenomes";
+ return DBRefSource.ENSEMBLGENOMES;
}
@Override
@Override
public String getDbSource()
{
- return "EnsemblGenomes";
+ return DBRefSource.ENSEMBLGENOMES;
}
}
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST);
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
BufferedReader br = null;
try
{
- URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST);
+ URL url = getDivisionsUrl(ensemblGenomesDomain);
if (url != null)
{
br = getHttpResponse(url, null);
}
- parseResponse(br, ENSEMBL_GENOMES_REST);
+ parseResponse(br, ensemblGenomesDomain);
} catch (IOException e)
{
// ignore
*/
public String getGeneId(String identifier)
{
- return parseGeneId(getResult(identifier, null));
+ return getGeneId(identifier, null);
+ }
+
+ /**
+ * Returns the gene id related to the given identifier (which may be for a
+ * gene, transcript or protein)
+ *
+ * @param identifier
+ * @param objectType
+ * @return
+ */
+ public String getGeneId(String identifier, String objectType)
+ {
+ return parseGeneId(getResult(identifier, objectType));
+ }
+
+ /**
+ * Parses the JSON response and returns the gene identifier, or null if not
+ * found. If the returned object_type is Gene, returns the id, if Transcript
+ * returns the Parent. If it is Translation (peptide identifier), then the
+ * Parent is the transcript identifier, so we redo the search with this value.
+ *
+ * @param br
+ * @return
+ */
+ protected String parseGeneId(JSONObject val)
+ {
+ String geneId = null;
+ String type = val.get(OBJECT_TYPE).toString();
+ if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+ {
+ // got the gene - just returns its id
+ geneId = val.get(JSON_ID).toString();
+ }
+ else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+ {
+ // got the transcript - return its (Gene) Parent
+ geneId = val.get(PARENT).toString();
+ }
+ else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+ {
+ // got the protein - get its Parent, restricted to type Transcript
+ String transcriptId = val.get(PARENT).toString();
+ geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+ }
+
+ return geneId;
}
/**
try
{
URL url = getUrl(identifier, objectType);
+
if (url != null)
{
br = getHttpResponse(url, ids);
}
/**
- * Parses the JSON response and returns the gene identifier, or null if not
- * found. If the returned object_type is Gene, returns the id, if Transcript
- * returns the Parent. If it is Translation (peptide identifier), then the
- * Parent is the transcript identifier, so we redo the search with this value,
- * specifying that object_type should be Transcript.
- *
- * @param jsonObject
- * @return
- */
- protected String parseGeneId(JSONObject json)
- {
- if (json == null)
- {
- // e.g. lookup failed with 404 not found
- return null;
- }
-
- String geneId = null;
- String type = json.get(OBJECT_TYPE).toString();
- if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
- {
- // got the gene - just returns its id
- geneId = json.get(JSON_ID).toString();
- }
- else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
- {
- // got the transcript - return its (Gene) Parent
- geneId = json.get(PARENT).toString();
- }
- else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
- {
- // got the protein - look up its Parent, restricted to type Transcript
- String transcriptId = json.get(PARENT).toString();
- geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT));
- }
-
- return geneId;
- }
-
- /**
* Calls the /lookup/id rest service for the given id, and if successful,
* parses and returns the gene's chromosomal coordinates
*
static
{
domainData = new HashMap<>();
- domainData.put(ENSEMBL_REST,
- new EnsemblData(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
- domainData.put(ENSEMBL_GENOMES_REST, new EnsemblData(
- ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_BASEURL,
+ new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
+ DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
}
protected volatile boolean inProgress = false;
*/
public EnsemblRestClient()
{
- this(ENSEMBL_REST);
+ super();
+
+ /*
+ * initialise domain info lazily
+ */
+ if (!domainData.containsKey(ensemblDomain))
+ {
+ domainData.put(ensemblDomain,
+ new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
+ }
+ if (!domainData.containsKey(ensemblGenomesDomain))
+ {
+ domainData.put(ensemblGenomesDomain, new EnsemblData(
+ ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ }
}
/**
boolean checkEnsembl()
{
BufferedReader br = null;
+ String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
try
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
- URL ping = new URL(getDomain() + "/info/ping" + CONTENT_TYPE_JSON);
+ URL ping = new URL(pingUrl);
/*
* expect {"ping":1} if ok
} catch (Throwable t)
{
System.err.println(
- "Error connecting to " + PING_URL + ": " + t.getMessage());
+ "Error connecting to " + pingUrl + ": " + t.getMessage());
} finally
{
if (br != null)
*/
package jalview.ext.ensembl;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
*/
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
{
+ // domain properties lookup keys:
+ protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
+
+ protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
+
+ // domain properties default values:
+ protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
+
+ protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "https://rest.ensemblgenomes.org";
+
/*
* accepts ENSG/T/E/P with 11 digits
* or ENSMUSP or similar for other species
"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+ "(CCDS[0-9.]{3,}$)");
- protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+ protected final String ensemblGenomesDomain;
- protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+ protected final String ensemblDomain;
protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
constrained, regulatory
}
- private String domain = ENSEMBL_REST;
+ private String domain;
+
+ /**
+ * Constructor
+ */
+ public EnsemblSequenceFetcher()
+ {
+ /*
+ * the default domain names may be overridden in .jalview_properties;
+ * this allows an easy change from http to https in future if needed
+ */
+ ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
+ DEFAULT_ENSEMBL_BASEURL);
+ ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+ DEFAULT_ENSEMBL_GENOMES_BASEURL);
+ domain = ensemblDomain;
+ }
@Override
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+ if (ensemblGenomesDomain.equals(getDomain()))
{
return DBRefSource.ENSEMBLGENOMES;
}
continue;
}
- int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
if (mapping[m].getSequence() == sequence[pdbfnum][s]
&& (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
{
+ int lastPos = StructureMapping.UNASSIGNED_VALUE;
SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
- if (pos < 1 || pos == lastPos)
+ if (pos == lastPos)
{
continue;
}
+ if (pos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ // terminate current colour op
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+ // reset lastPos
+ lastPos = StructureMapping.UNASSIGNED_VALUE;
+ continue;
+ }
lastPos = pos;
// TODO: deal with case when buffer is too large for Jmol to parse
// - execute command and flush
- command.append(";");
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+
if (command.length() > 51200)
{
// add another chunk
package jalview.fts.service.uniprot;
+import jalview.bin.Cache;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
public class UniProtFTSRestClient extends FTSRestClient
{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
private static FTSRestClientI instance = null;
- public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+ public final String uniprotSearchEndpoint;
+
+ public UniProtFTSRestClient()
+ {
+ super();
+ uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+ DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+ }
@Override
public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
}
WebResource webResource = null;
- webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
+ webResource = client.resource(uniprotSearchEndpoint)
.queryParam("format", "tab")
.queryParam("columns", wantedFields)
.queryParam("limit", String.valueOf(responseSize))
String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
if (foundDataRow != null && foundDataRow.length > 0)
{
- result = new ArrayList<FTSData>();
+ result = new ArrayList<>();
boolean firstRow = true;
for (String dataRow : foundDataRow)
{
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.Option;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Scanner;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
+ Map<String, Float> distribution = new HashMap<>(); // temporary
+
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
AlignViewport viewport;
public AlignViewControllerI avc;
+ /*
+ * The selected HMM for this align frame
+ */
+ SequenceI selectedHMMSequence;
List<AlignmentPanel> alignPanels = new ArrayList<>();
*/
String fileName = null;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
+ ap.av.initInformationWorker(ap);
}
}
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ showInformationHistogram.setSelected(av.isShowInformationHistogram());
+ showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+ normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
}
@Override
+ public void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ if (!alignmentIsSufficient(1))
+ {
+ return;
+ }
+ List<ArgumentI> args = new ArrayList<>();
+ if (withDefaults)
+ {
+ // todo: construct this in HMMERPreset?
+ String argName = MessageManager.getString("label.hmmbuild_for");
+ String argValue = MessageManager.getString("label.alignment");
+ args.add(
+ new Option(argName, null, false, null, argValue, null, null));
+ }
+ else
+ {
+ WsParamSetI set = new HMMERPreset();
+ ParamDatastoreI store = HMMERParamStore.forBuild();
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMBuild(this, args)).start();
+ }
+
+ @Override
+ public void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
+ {
+ return;
+ }
+ List<ArgumentI> args = new ArrayList<>();
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ ParamDatastoreI store = HMMERParamStore.forAlign();
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMAlign(this, args)).start();
+ }
+
+ @Override
+ public void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ if (!checkForHMM())
+ {
+ return;
+ }
+ List<ArgumentI> args = new ArrayList<>();
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ ParamDatastoreI store = HMMERParamStore.forSearch();
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMSearch(this, args)).start();
+ alignPanel.repaint();
+ }
+
+ /**
+ * Checks if the frame has a selected hidden Markov model
+ *
+ * @return
+ */
+ private boolean checkForHMM()
+ {
+ if (getSelectedHMM() == null)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Checks if the alignment contains the required number of sequences.
+ *
+ * @param required
+ * @return
+ */
+ public boolean alignmentIsSufficient(int required)
+ {
+ if (getViewport().getAlignment().getSequences().size() < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.not_enough_sequences"));
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public void addDatabase_actionPerformed() throws IOException
+ {
+ if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+ }
+
+ String path = openFileChooser(false);
+ if (new File(path).exists())
+ {
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+ if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+ || format == FileFormat.Pfam)
+ {
+ String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ String currentDbPaths = Cache
+ .getProperty(Preferences.HMMSEARCH_DB_PATHS);
+ currentDbPaths += " " + path;
+
+ String fileName = StringUtils.getLastToken(path, File.separator);
+ Scanner scanner = new Scanner(fileName).useDelimiter(".");
+ String name = scanner.next();
+ scanner.close();
+ currentDbs += " " + path; // TODO remove path from file name
+ scanner.close();
+
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.invalid_format"));
+ }
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.not_enough_sequences"));
+ }
+ }
+
+ /**
+ * Opens a file chooser
+ *
+ * @param forFolder
+ * @return
+ */
+ protected String openFileChooser(boolean forFolder)
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
@Override
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
@Override
protected void copy_actionPerformed(ActionEvent e)
{
- System.gc();
if (viewport.getSelectionGroup() == null)
{
return;
return;
}
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
- ArrayList<int[]> hiddenRegions = viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy();
- for (int[] region : hiddenRegions)
- {
- if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
- {
- hiddenColumns
- .add(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ hiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
Desktop.jalviewClipboard = new Object[] { seqs,
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
+ * @throws InterruptedException
+ * @throws IOException
*/
- void paste(boolean newAlignment)
+ void paste(boolean newAlignment) throws IOException, InterruptedException
{
boolean externalPaste = true;
try
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int[] region : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
-
}
@Override
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int region[] : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
*
* @param file
* either a filename or a URL string.
+ * @throws InterruptedException
+ * @throws IOException
*/
public void loadJalviewDataFile(String file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
- SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
- viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- viewport.getAlignment().setHiddenColumns(cs);
+ viewport.getAlignment().setupJPredAlignment();
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
}
if (isAnnotation)
{
-
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
MessageManager.getString("option.trim_retrieved_seqs"));
trimrs.setToolTipText(
MessageManager.getString("label.trim_retrieved_sequences"));
- trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.setSelected(
+ Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
- Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
};
});
}
}
+ /**
+ * Sets the status of the HMMER menu
+ */
+ public void updateHMMERStatus()
+ {
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getSelectedHMM()
+ {
+ if (selectedHMMSequence == null)
+ {
+ return null;
+ }
+ return selectedHMMSequence.getHMM();
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public SequenceI getSelectedHMMSequence()
+ {
+ return selectedHMMSequence;
+ }
+
+ /**
+ * Sets the selected hidden Markov model
+ *
+ * @param selectedHMM
+ */
+ public void setSelectedHMMSequence(SequenceI selectedHMM)
+ {
+ this.selectedHMMSequence = selectedHMM;
+ hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
+ + selectedHMM.getHMM().getName());
+ hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
+ + selectedHMM.getHMM().getName());
+ }
+
+ @Override
+ public void hmmerMenu_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup grp = getViewport().getSelectionGroup();
+ if (grp != null)
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
+ + grp.getName());
+ }
+ else
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild")
+ + " from Alignment");
+ }
+ }
+
@Override
protected void loadVcf_actionPerformed()
{
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
private AnnotationColumnChooser annotationColumnSelectionState;
+ boolean validCharWidth;
+
+ public boolean followSelection = true;
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
/**
* Creates a new AlignViewport object.
*
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ AlignmentI al = getAlignment();
+ al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (hconsensus == null && !isDataset)
+ if (consensusProfiles == null && !isDataset)
{
- if (!alignment.isNucleotide())
+ if (!al.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
+ // for now, use consensus options for Information till it gets its own
+ setShowHMMSequenceLogo(showSequenceLogo);
+ setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+ setShowInformationHistogram(showConsensusHistogram);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide()
+ // initInformation();
+
+ String colourProperty = al.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(alignment, schemeName);
+ .getColourScheme(al, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
- boolean validCharWidth;
-
/**
* {@inheritDoc}
*/
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (getAlignment() != null && align != null)
{
- alignment.setCodonFrames(align.getCodonFrames());
+ getAlignment().setCodonFrames(align.getCodonFrames());
}
}
}
/**
- * returns the visible column regions of the alignment
+ * Returns an iterator over the visible column regions of the alignment
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
* area
* @return
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- int[] viscontigs = null;
- int start = 0, end = 0;
+ int start = 0;
+ int end = 0;
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
}
else
{
- end = alignment.getWidth();
+ end = getAlignment().getWidth();
}
- viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
- return viscontigs;
+
+ return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+ end, false);
}
/**
return false;
}
- public boolean followSelection = true;
-
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
.getStructureSelectionManager(Desktop.instance);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
-
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
}
fr.setTransparency(featureSettings.getTransparency());
}
+
}
if (av.hasHiddenColumns())
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- start = hidden.findColumnPosition(start);
- end = hidden.findColumnPosition(end);
+ start = hidden.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(end);
if (start == end)
{
if (!hidden.isVisible(r[0]))
{
// reset the width to exclude hidden columns
width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
+ .absoluteToVisibleColumn(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@Override
public void paintComponent(Graphics g)
{
- invalidate();
+ invalidate(); // needed so that the id width adjuster works correctly
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
+
+ validate(); // needed so that the id width adjuster works correctly
/*
- * set scroll bar positions
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
*/
ViewportRanges ranges = av.getRanges();
setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int resWidth = getSeqPanel().seqCanvas
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
+ .absoluteToVisibleColumn(maxwidth);
}
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int height = ((maxwidth / chunkWidth) + 1) * cHeight;
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- /*
- * To avoid jumpy vertical scrolling (if some sequences are gapped or not
- * mapped), we can make the scroll-to location a sequence above the one
- * actually mapped.
- */
- SequenceI mappedTo = sr.getResults().get(0).getSequence();
- List<SequenceI> seqs = av.getAlignment().getSequences();
-
- /*
- * This is like AlignmentI.findIndex(seq) but here we are matching the
- * dataset sequence not the aligned sequence
- */
- boolean matched = false;
- for (SequenceI seq : seqs)
- {
- if (mappedTo == seq.getDatasetSequence())
- {
- matched = true;
- break;
- }
- }
- if (!matched)
- {
- return; // failsafe, shouldn't happen
- }
-
- /*
- * Scroll to position but centring the target residue.
- */
scrollToPosition(sr, verticalOffset, true, true);
}
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.workers.InformationThread;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.MediaTracker;
import java.awt.RenderingHints;
import java.awt.Toolkit;
import java.awt.datatransfer.StringSelection;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.Iterator;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
public class AnnotationLabels extends JPanel
implements MouseListener, MouseMotionListener, ActionListener
{
- // width in pixels within which height adjuster arrows are shown and active
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
private static final String COPYCONS_SEQ = MessageManager
.getString("label.copy_consensus_sequence");
- private static Image adjusterImage;
-
- private static int adjusterImageHeight;
-
private final boolean debugRedraw = false;
private AlignmentPanel ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
- if (adjusterImage == null)
- {
- loadAdjusterImage();
- }
-
addMouseListener(this);
addMouseMotionListener(this);
addMouseWheelListener(ap.getAnnotationPanel());
}
/**
- * Loads the gif for the panel height adjustment
- */
- protected void loadAdjusterImage()
- {
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
- Image temp = null;
-
- if (url != null)
- {
- temp = Toolkit.getDefaultToolkit().createImage(url);
- }
-
- try
- {
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(temp, 0);
- mt.waitForID(0);
- } catch (Exception ex)
- {
- }
-
- BufferedImage bi = new BufferedImage(temp.getHeight(this),
- temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
- Graphics2D g = (Graphics2D) bi.getGraphics();
- g.rotate(Math.toRadians(90));
- g.drawImage(temp, 0, -bi.getWidth(this), this);
- adjusterImage = bi;
- adjusterImageHeight = bi.getHeight();
- }
-
- /**
* DOCUMENT ME!
*
* @param y
pop.show(this, evt.getX(), evt.getY());
return;
}
+
+ final AlignmentAnnotation ann = aa[selectedRow];
+ final boolean isSequenceAnnotation = ann.sequenceRef != null;
+
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
if (selectedRow < aa.length)
{
- if (aa[selectedRow].sequenceRef != null)
+ if (isSequenceAnnotation)
{
- final String label = aa[selectedRow].label;
+ final String label = ann.label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " "
+ label;
AlignmentUtils.showOrHideSequenceAnnotations(
ap.av.getAlignment(), Collections.singleton(label),
null, false, false);
- // for (AlignmentAnnotation ann : ap.av.getAlignment()
- // .getAlignmentAnnotation())
- // {
- // if (ann.sequenceRef != null && ann.label != null
- // && ann.label.equals(label))
- // {
- // ann.visible = false;
- // }
- // }
ap.refresh(true);
}
});
// property methods
if (selectedRow < aa.length)
{
- final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
+ final String label = ann.label;
+ if (!(ann.autoCalculated)
+ && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
{
- if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ if (ann.graph == AlignmentAnnotation.NO_GRAPH)
{
// display formatting settings for this row.
pop.addSeparator();
// av and sequencegroup need to implement same interface for
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
- aa[selectedRow].scaleColLabel);
+ ann.scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
}
else if (label.indexOf("Consensus") > -1)
{
- pop.addSeparator();
- // av and sequencegroup need to implement same interface for
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null)
- ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
- : ap.av.isIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
- cbmi.addActionListener(new ActionListener()
+ addConsensusMenu(pop, ann);
+ }
+ else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ addHmmerMenu(pop, ann);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * Adds context menu options for (alignment or group) Hmmer annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString(
+ "label.ignore_below_background_frequency"),
+ isGroupAnnotation
+ ? ann.groupRef
+ .isIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!ann.groupRef.isUseInfoLetterHeight())
{
- if (aaa.groupRef != null)
- {
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel()
- .paint(ap.getAnnotationPanel().getGraphics());
- }
- else
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- ap.alignmentChanged();
+ ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ // todo and recompute group annotation
}
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
- if (aaa.groupRef != null)
+ }
+ else if (!ap.av.isInfoLetterHeight())
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setShowConsensusHistogram(chist.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
- aa[selectedRow].groupRef.isShowSequenceLogo());
- cprofl.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setshowSequenceLogo(cprofl.getState());
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofl);
- final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
- aa[selectedRow].groupRef.isNormaliseSequenceLogo());
- cproflnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged(); // todo not like this
+ }
+ });
+ pop.add(cbmi);
+ final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+ MessageManager.getString("label.use_info_for_height"),
+ isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+ : ap.av.isInfoLetterHeight());
+ letterHeight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+ ann.groupRef.setIgnoreBelowBackground(true);
+ // todo and recompute group annotation
+ }
+ else
+ {
+ ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+ ap.av.setIgnoreBelowBackground(true, ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(letterHeight);
+ if (isGroupAnnotation)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setShowHMMSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowHMMSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseHMMSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
- // automatically enable logo display if we're clicked
- aaa.groupRef.setshowSequenceLogo(true);
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cproflnorm);
+ /**
+ * Adds context menu options for (alignment or group) Consensus annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addConsensusMenu(JPopupMenu pop,
+ final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (ann.groupRef != null)
+ ? ann.groupRef.isIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setIgnoreGapsConsensus(cbmi.getState());
}
else
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"),
- av.isShowSequenceLogo());
- cprof.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprof);
- final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"),
- av.isNormaliseSequenceLogo());
- cprofnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(true);
- av.setNormaliseSequenceLogo(cprofnorm.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofnorm);
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
+ ap.alignmentChanged();
}
+ });
+ pop.add(cbmi);
+ if (isGroupAnnotation)
+ {
+ /*
+ * group consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
}
- pop.show(this, evt.getX(), evt.getY());
+ else
+ {
+ /*
+ * alignment consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
}
/**
protected void showOrHideAdjuster(MouseEvent evt)
{
boolean was = resizePanel;
- resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
if (resizePanel != was)
{
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
-
}
}
return;
Alignment ds = new Alignment(dseqs);
if (av.hasHiddenColumns())
{
- omitHidden = av.getAlignment().getHiddenColumns()
- .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+ Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+ .getVisContigsIterator(0, sq.getLength(), false);
+ omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
if (av.hasHiddenColumns())
{
- hiddenColumns = av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy();
+ hiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
@Override
public void paintComponent(Graphics g)
{
-
int width = getWidth();
if (width == 0)
{
}
drawComponent(g2, true, width);
-
}
/**
}
}
- if (resizePanel)
- {
- // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this);
- }
- else if (dragEvent != null && aa != null)
+ if (!resizePanel && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
if (e.isShiftDown())
{
e.consume();
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
av.getRanges().scrollRight(true);
}
- else
+ else if (wheelRotation < 0)
{
av.getRanges().scrollRight(false);
}
if (av.hasHiddenColumns())
{
column = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(column);
+ .visibleToAbsoluteColumn(column);
}
AlignmentAnnotation ann = aa[row];
{
this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
}
+ else
+ {
+ this.setToolTipText(null); // no tooltip if null or empty description
+ }
}
else
{
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
gg.fillRect(0, 0, imgWidth, image.getHeight());
imageFresh = true;
}
-
+
drawComponent(gg, av.getRanges().getStartRes(),
av.getRanges().getEndRes() + 1);
imageFresh = false;
int er = av.getRanges().getEndRes() + 1;
int transX = 0;
- long stime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
- long mtime = System.currentTimeMillis();
if (horizontal > 0) // scrollbar pulled right, image to the left
{
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
- long dtime = System.currentTimeMillis();
+
fastPaint = true;
- repaint();
- long rtime = System.currentTimeMillis();
- if (debugRedraw)
- {
- System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
- + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
- + "\tRepaint call:\t" + (rtime - dtime));
- }
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
}
private volatile boolean lastImageGood = false;
import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Color;
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/*
* the most recently opened PCA results panel
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
/*
* now we can actually add entries to the combobox,
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
*/
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
*/
protected void openPcaPanel(String modelName, SimilarityParamsI params)
{
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
/*
* gui validation shouldn't allow insufficient sequences here, but leave
*/
final String name = scheme.getSchemeName();
String label = MessageManager.getStringOrReturn(
- "label.colourScheme_" + name.toLowerCase().replace(" ", "_"),
- name);
+ "label.colourScheme_", name.toLowerCase().replace(" ", "_"));
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
label);
radioItem.setName(name);
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
+ frame.setOpaque(false);
if (frame.getX() < 1 && frame.getY() < 1)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
-
- System.gc();
};
});
{
ssm.resetAll();
}
- System.gc();
}
@Override
return;
}
- AlignmentViewport source = null, target = null;
+ AlignViewportI source = null;
+ AlignViewportI target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
public void invertSelection()
{
- for (int i = 0; i < table.getRowCount(); i++)
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+ for (int i = 0; i < data.length; i++)
{
- Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
- table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+ data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
}
+ updateFeatureRenderer(data, true);
+ table.repaint();
}
public void orderByAvWidth()
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
av.getRanges().addPropertyChangeListener(this);
- }
+ }
/**
* DOCUMENT ME!
gg.translate(0, -transY);
fastPaint = true;
- repaint();
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
}
/**
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
-
+
if (fastPaint)
{
fastPaint = false;
g.drawImage(image, 0, 0, this);
-
+
return;
}
-
+
int oldHeight = imgHeight;
-
+
imgHeight = getHeight();
imgHeight -= (imgHeight % av.getCharHeight());
-
+
if (imgHeight < 1)
{
return;
}
-
+
if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
{
- image = new BufferedImage(getWidth(), imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
}
-
+
gg = (Graphics2D) image.getGraphics();
-
+
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
-
+
drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
-
+
g.drawImage(image, 0, 0, this);
}
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int annotationHeight = 0;
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
if (e.isShiftDown())
{
av.getRanges().scrollUp(false);
}
}
- else
+ else if (wheelRotation < 0)
{
if (e.isShiftDown())
{
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Graphics;
-import java.awt.Image;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
int oldX = 0;
- Image image;
-
AlignmentPanel ap;
/**
public IdwidthAdjuster(AlignmentPanel ap)
{
this.ap = ap;
-
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
-
- if (url != null)
- {
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
- }
-
+ setBackground(Color.white);
addMouseListener(this);
addMouseMotionListener(this);
}
if (active)
{
- if (image != null)
- {
- // g.drawImage(image, getWidth() - 20, 2, this);
setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
- }
- else
- {
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
- }
}
}
}
jGroup.setTextCol2(sg.textColour2.getRGB());
jGroup.setTextColThreshold(sg.thresholdTextColour);
jGroup.setShowUnconserved(sg.getShowNonconserved());
- jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
}
else
{
- ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
- for (int[] region : hiddenRegions)
+ Iterator<int[]> hiddenRegions = hidden.iterator();
+ while (hiddenRegions.hasNext())
{
+ int[] region = hiddenRegions.next();
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
view.getIgnoreGapsinConsensus());
af.viewport.getResidueShading()
- .setConsensus(af.viewport.getSequenceConsensusHash());
+ .setConsensus(af.viewport.getConsensusProfiles());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
true);
af.viewport.getResidueShading()
- .setConsensus(af.viewport.getSequenceConsensusHash());
+ .setConsensus(af.viewport.getConsensusProfiles());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
import jalview.ws.params.ParameterI;
import jalview.ws.params.ValueConstrainI;
import jalview.ws.params.ValueConstrainI.ValueType;
+import jalview.ws.params.simple.LogarithmicParameter;
import java.awt.BorderLayout;
import java.awt.Component;
public class ParamBox extends JPanel
implements ChangeListener, ActionListener, MouseListener
{
+
+ boolean isLogarithmic;
+
boolean adjusting = false;
boolean choice = false;
choice = true;
}
}
+ if (parm instanceof LogarithmicParameter)
+ {
+ isLogarithmic = true;
+ }
if (!compact)
{
{
if (!adjusting)
{
- valueField.setText("" + ((integ) ? ("" + slider.getValue())
- : ("" + slider.getValue() / 1000f)));
+ if (!isLogarithmic)
+ {
+ valueField.setText("" + ((integ) ? ("" + slider.getValue())
+ : ("" + slider.getValue() / 1000f)));
+ }
+ else
+ {
+ Double base = ((LogarithmicParameter) parameter).getBase();
+ Double value = Math.pow(
+ base,
+ slider.getValue() / 1000000f);
+ valueField.setText(formatDouble(value));
+ }
checkIfModified();
}
}
+ public String formatDouble(Double value)
+ {
+ String string = String.format("%3.3f", value);
+ if (value < 0.001)
+ {
+ string = String.format("%3.3e", value);
+ }
+ return string;
+ }
+
public void updateControls(ParameterI parm)
{
adjusting = true;
}
else
{
- valueField.setText(parm.getValue());
+ if (parm instanceof LogarithmicParameter)
+ {
+ Double base = ((LogarithmicParameter) parm).getBase();
+ Double value = Math.pow(base,
+ Double.parseDouble(parm.getValue()) / 1000000);
+ valueField.setText(formatDouble(value));
+ }
+ else
+ {
+ valueField.setText(parm.getValue());
+ }
}
}
lastVal = updateSliderFromValueField();
{
int iVal;
float fVal;
+ double dVal;
if (validator != null)
{
if (integ)
}
return new int[] { iVal };
}
+ else if (isLogarithmic)
+ {
+ double eValue;
+ dVal = 0d;
+ try
+ {
+ valueField.setText(valueField.getText().trim());
+ eValue = Double.valueOf(valueField.getText());
+
+ dVal = Math.log(eValue) / Math
+ .log(((LogarithmicParameter) parameter).getBase())
+ * 1000000;
+
+ if (validator.getMin() != null
+ && validator.getMin().doubleValue() > dVal)
+ {
+ dVal = validator.getMin().doubleValue();
+ // TODO: provide visual indication that hard limit was reached for
+ // this parameter
+ // update value field to reflect any bound checking we performed.
+ valueField.setText("" + formatDouble(eValue));
+ }
+ if (validator.getMax() != null
+ && validator.getMax().doubleValue() < dVal)
+ {
+ dVal = validator.getMax().doubleValue();
+ // TODO: provide visual indication that hard limit was reached for
+ // this parameter
+ // update value field to reflect any bound checking we performed.
+ valueField.setText("" + formatDouble(eValue));
+ }
+ } catch (Exception e)
+ {
+ }
+ ;
+ if (validator.getMin() != null && validator.getMax() != null)
+ {
+ slider.getModel().setRangeProperties((int) (dVal), 1,
+ (int) (validator.getMin().doubleValue()),
+ 1 + (int) (validator.getMax().doubleValue()),
+ true);
+ }
+ else
+ {
+ slider.setVisible(false);
+ }
+ return new double[] { dVal };
+ }
else
{
fVal = 0f;
URL linkImageURL = getClass().getResource("/images/link.gif");
- Map<String, OptionBox> optSet = new java.util.LinkedHashMap<String, OptionBox>();
+ Map<String, OptionBox> optSet = new java.util.LinkedHashMap<>();
- Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<String, ParamBox>();
+ Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<>();
public Map<String, OptionBox> getOptSet()
{
*/
public List<ArgumentI> getCurrentSettings()
{
- List<ArgumentI> argSet = new ArrayList<ArgumentI>();
+ List<ArgumentI> argSet = new ArrayList<>();
for (OptionBox opts : getOptSet().values())
{
OptionI opt = opts.getOptionIfEnabled();
od.getColumns(av.getAlignment()));
mg.translate(0, -od.getSequencesHeight());
}
- System.gc();
or.removePropertyChangeListener(progressPanel);
or = null;
@Override
public void paintComponent(Graphics g)
{
- // super.paintComponent(g);
+ super.paintComponent(g);
if (restart)
{
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.renderer.OverviewRenderer;
import jalview.util.MessageManager;
private OverviewCanvas oviewCanvas;
- private AlignViewport av;
+ private AlignViewportI av;
private AlignmentPanel ap;
@Override
public void mouseMoved(MouseEvent evt)
{
- if (od.isPositionInBox(evt.getX(), evt.getY()))
+ if (!draggingBox)
+ // don't bother changing the cursor if we're dragging the box
+ // as we can't have moved inside or out of the box in that case
{
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- }
- else
- {
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ }
}
}
});
if (!od.isPositionInBox(evt.getX(), evt.getY()))
{
draggingBox = false;
+
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
showPopupMenu(evt);
}
}
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ draggingBox = false;
+ }
+
});
}
package jalview.gui;
import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPairwiseAlignPanel;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
import java.awt.event.ActionEvent;
import java.util.Vector;
private static final String DASHES = "---------------------\n";
- AlignmentViewport av;
+ AlignViewportI av;
Vector<SequenceI> sequences;
* Creates a new PairwiseAlignPanel object.
*
* @param viewport
- * DOCUMENT ME!
*/
- public PairwiseAlignPanel(AlignmentViewport viewport)
+ public PairwiseAlignPanel(AlignViewportI viewport)
{
super();
this.av = viewport;
- sequences = new Vector<SequenceI>();
+ sequences = new Vector<>();
SequenceGroup selectionGroup = viewport.getSelectionGroup();
boolean isSelection = selectionGroup != null
JMenuItem sequenceFeature = new JMenuItem();
+
JMenuItem textColour = new JMenuItem();
JMenu jMenu1 = new JMenu();
* currently selected sequence (if there is one):
*/
final List<SequenceI> selectedSequence = (seq == null
- ? Collections.<SequenceI> emptyList()
- : Arrays.asList(seq));
+ ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
+
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
});
add(menuItem);
+ if (sequence.isHMMConsensusSequence())
+ {
+ JMenuItem selectHMM = new JCheckBoxMenuItem();
+ selectHMM.setText(MessageManager.getString("label.select_hmm"));
+ selectHMM.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ selectHMM_actionPerformed(sequence);
+ }
+ });
+ add(selectHMM);
+ }
+
if (alignPanel.av.getSelectionGroup() != null
&& alignPanel.av.getSelectionGroup().getSize() > 1)
{
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+ Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
jMenu1.add(displayNonconserved);
}
+ protected void selectHMM_actionPerformed(SequenceI seq)
+ {
+ // TODO move this to Viewport
+ if (seq.isHMMConsensusSequence())
+ {
+ ap.alignFrame.setSelectedHMMSequence(seq);
+ }
+ }
+
/**
* Constructs the entries for the colour menu
*/
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
-
- HiddenColumns hidden = new HiddenColumns();
- BitSet inserts = new BitSet(), mask = new BitSet();
-
- // set mask to preserve existing hidden columns outside selected group
- if (ap.av.hasHiddenColumns())
- {
- ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
- }
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
- ap.av.getSelectionGroup().getEndRes() + 1);
-
- // and clear that part of the mask
- mask.andNot(inserts);
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
}
inserts.and(sq.getInsertionsAsBits());
}
- }
- else
- {
- // initially, mark all columns to be hidden
- inserts.set(0, ap.av.getAlignment().getWidth());
-
- // and clear out old hidden regions completely
- mask.clear();
+ hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
- if (!markedPopup && sequence != null)
+ else if (!markedPopup && sequence != null)
{
- inserts.and(sequence.getInsertionsAsBits());
- }
+ inserts.or(sequence.getInsertionsAsBits());
- // finally, preserve hidden regions outside selection
- inserts.or(mask);
-
- // and set hidden columns accordingly
- hidden.hideMarkedBits(inserts);
-
- ap.av.getAlignment().setHiddenColumns(hidden);
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HmmerCommand;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String HMMER_PATH = "HMMER_PATH";
+
+ public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
+
+ public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+
+ /*
* Set Visual tab defaults
*/
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
showConsensLogo
.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
userIdWidth.setText(wi == null ? "" : wi.toString());
// TODO: refactor to use common enum via FormatAdapter and allow extension
// for new flat file formats
Boolean.toString(showConsensHistogram.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+ Boolean.toString(showHMMLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
maxColour.getBackground());
/*
+ * Save HMMER settings
+ */
+ Cache.applicationProperties.setProperty("TRIM_TERMINI",
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty("USE_UNIPROT",
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+ hmmerSequenceCount.getText());
+ Cache.applicationProperties.setProperty(HMMER_PATH,
+ hmmerPath.getText());
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
* Save Overview settings
*/
Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
&& (identity.isSelected() || showGroupConsensus.isSelected()));
showConsensLogo.setEnabled(annotations.isSelected()
&& (identity.isSelected() || showGroupConsensus.isSelected()));
+ showInformationHistogram.setEnabled(annotations.isSelected());
+ showHMMLogo.setEnabled(annotations.isSelected());
}
@Override
}
return true;
}
+
+ /**
+ * Returns true if hmmer path is to a folder that contains an executable
+ * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+ * dialog)
+ */
+ @Override
+ protected boolean validateHMMERPath(boolean showWarning)
+ {
+ String folder = hmmerPath.getText().trim();
+
+ if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+ {
+ return true;
+ }
+ if (showWarning && folder.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.hmmbuild_not_found"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+
+ /**
+ * Checks if a file can be executed
+ *
+ * @param path
+ * the path to the file
+ * @return
+ */
+ public boolean canExecute(String path)
+ {
+ File file = new File(path);
+ if (!file.canExecute())
+ {
+ file = new File(path + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
boolean applyToAllViews = false;
- // Controller controller;
public RotatableCanvas(AlignmentPanel ap)
{
this.av = ap.av;
addMouseWheelListener(new MouseWheelListener()
{
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
+ /*
+ * zoom in
+ */
scale = (float) (scale * 1.1);
repaint();
}
-
- else
+ else if (wheelRotation < 0)
{
+ /*
+ * zoom out
+ */
scale = (float) (scale * 0.9);
repaint();
}
boolean first = true;
+ @Override
public void setPoints(Vector points, int npoint)
{
this.points = points;
dim = height;
}
- return (float) ((dim * scalefactor) / (2 * maxwidth));
+ return (dim * scalefactor) / (2 * maxwidth);
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g1)
{
for (int i = 0; i < npoint; i++)
{
SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
+ int y = (int) ((sp.coord[1] - centre[1]) * scale)
+ halfheight;
float z = sp.coord[1] - centre[2];
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void keyTyped(KeyEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void keyReleased(KeyEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_UP)
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
// controller.handleSequenceSelectionEvent(new
// SequenceSelectionEvent(this,sel));
// }
+ @Override
public void mouseMoved(MouseEvent evt)
{
SequenceI found = findPoint(evt.getX(), evt.getY());
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
mx = evt.getX();
{
rotmat.setIdentity();
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
+ rotmat.rotate(my - omy, 'x');
+ rotmat.rotate(mx - omx, 'y');
for (int i = 0; i < npoint; i++)
{
{
SequencePoint sp = (SequencePoint) points.elementAt(i);
int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
- + ((float) getWidth() / 2.0));
+ + (getWidth() / 2.0));
int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
- + ((float) getHeight() / 2.0));
+ + (getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
for (int i = 0; i < npoint; i++)
{
SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+ int px = (int) ((sp.coord[0] - centre[0]) * scale)
+ halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord[1] - centre[1]) * scale)
+ halfheight;
if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
import javax.swing.JMenuItem;
if (av.hasHiddenColumns())
{
- x = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+ x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
}
if (x >= av.getAlignment().getWidth())
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasHiddenColumns())
+ if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
{
item = new JMenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
if (res >= av.getAlignment().getWidth())
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
res = Math.max(0, res);
- res = hidden.adjustForHiddenColumns(res);
+ res = hidden.visibleToAbsoluteColumn(res);
res = Math.min(res, av.getAlignment().getWidth() - 1);
min = Math.min(res, min);
max = Math.max(res, max);
reveal = av.getAlignment().getHiddenColumns()
.getRegionWithEdgeAtRes(res);
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
ToolTipManager.sharedInstance().registerComponent(this);
this.setToolTipText(
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
/*
* shouldn't get called in wrapped mode as the scale above is
* drawn instead by SeqCanvas.drawNorthScale
{
if (hidden.isVisible(sel))
{
- sel = hidden.findColumnPosition(sel);
+ sel = hidden.absoluteToVisibleColumn(sel);
}
else
{
if (av.getShowHiddenMarkers())
{
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+ startx + widthx + 1);
+ while (it.hasNext())
{
- res = pos - startx;
-
- if (res < 0 || res > widthx)
- {
- continue;
- }
+ res = it.next() - startx;
gg.fillPolygon(
new int[]
- { -1 + res * avCharWidth - avCharHeight / 4,
- -1 + res * avCharWidth + avCharHeight / 4,
- -1 + res * avCharWidth },
- new int[]
- { y, y, y + 2 * yOf }, 3);
+ { -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth }, new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
|| evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
// scroll event, repaint panel
- repaint();
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
}
}
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.Comparison;
import java.awt.Shape;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
import javax.swing.JComponent;
if (av.hasHiddenColumns())
{
HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
- startX = hiddenColumns.adjustForHiddenColumns(startx);
- endX = hiddenColumns.adjustForHiddenColumns(endx);
+ startX = hiddenColumns.visibleToAbsoluteColumn(startx);
+ endX = hiddenColumns.visibleToAbsoluteColumn(endx);
}
FontMetrics fm = getFontMetrics(av.getFont());
int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
-
+
gg.copyArea(horizontal * charWidth, vertical * charHeight,
img.getWidth(), img.getHeight(), -horizontal * charWidth,
-vertical * charHeight);
drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
gg.translate(-transX, -transY);
- repaint();
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the
+ // overview window and others may be adversely affected.
+ av.getAlignPanel().repaint();
} finally
{
fastpainting = false;
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
-
+
int width = getWidth();
int height = getHeight();
-
+
width -= (width % charWidth);
height -= (height % charHeight);
-
+
// selectImage is the selection group outline image
BufferedImage selectImage = drawSelectionGroup(
ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq());
-
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
}
-
+
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
}
-
+
gg.setColor(Color.white);
gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-
+
if (av.getWrapAlignment())
{
drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
-
+
// lcimg is a local *copy* of img which we'll draw selectImage on top of
BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
private BufferedImage buildLocalImage(BufferedImage selectImage)
{
// clone the cached image
- BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
- img.getType());
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+
+ // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ // img.getType());
Graphics2D g2d = lcimg.createGraphics();
g2d.drawImage(img, 0, 0, null);
try
{
- lcimg = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
} catch (OutOfMemoryError er)
{
System.gc();
int charWidth = av.getCharWidth();
g.setColor(Color.blue);
+ int res;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+
+ Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
+ endColumn);
+ while (it.hasNext())
{
- int res = pos - startColumn;
+ res = it.next() - startColumn;
if (res < 0 || res > endColumn - startColumn + 1)
{
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
+ .absoluteToVisibleColumn(maxwidth);
}
// chop the wrapped alignment extent up into panel-sized blocks and treat
else
{
int screenY = 0;
- final int screenYMax = endRes - startRes;
- int blockStart = startRes;
- int blockEnd = endRes;
+ int blockStart;
+ int blockEnd;
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
+ while (regions.hasNext())
+ {
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
/*
* draw up to just before the next hidden region, or the end of
* the visible region, whichever comes first
*/
- blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
- - screenY);
-
g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
* draw the downline of the hidden column marker (ScalePanel draws the
* triangle on top) if we reached it
*/
- if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
{
g1.setColor(Color.blue);
g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
-
- if (screenY > screenYMax)
- {
- // already rendered last block
- return;
- }
- }
-
- if (screenY <= screenYMax)
- {
- // remaining visible region to render
- blockEnd = blockStart + screenYMax - screenY;
- g1.translate(screenY * charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
- g1.translate(-screenY * charWidth, 0);
}
}
if (av.hasSearchResults())
{
SearchResultsI searchResults = av.getSearchResults();
- int[] visibleResults = searchResults.getResults(nextSeq,
- startRes, endRes);
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * charWidth, offset
- + ((i - startSeq) * charHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
}
// convert the cursorX into a position on the visible alignment
int cursor_xpos = av.getAlignment().getHiddenColumns()
- .findColumnPosition(cursorX);
+ .absoluteToVisibleColumn(cursorX);
if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
{
{
// package into blocks of visible columns
int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
+ int blockStart;
+ int blockEnd;
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy())
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
+ while (regions.hasNext())
{
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- blockEnd = hideStart - 1;
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
g.translate(screenY * charWidth, 0);
drawPartialGroupOutline(g, group,
g.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
-
- if (screenY > (endRes - startRes))
- {
- // already rendered last block
- break;
- }
- }
-
- if (screenY <= (endRes - startRes))
- {
- // remaining visible region to render
- blockEnd = blockStart + (endRes - startRes) - screenY;
- g.translate(screenY * charWidth, 0);
- drawPartialGroupOutline(g, group,
- blockStart, blockEnd, startSeq, endSeq, offset);
-
- g.translate(-screenY * charWidth, 0);
}
}
}
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
if (av.hasHiddenColumns())
{
firstCol = alignment.getHiddenColumns()
- .findColumnPosition(firstCol);
- lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ .absoluteToVisibleColumn(firstCol);
+ lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
scrollX = -range;
}
}
- // Both scrolling and resizing change viewport ranges: scrolling changes
- // both start and end points, but resize only changes end values.
- // Here we only want to fastpaint on a scroll, with resize using a normal
- // paint, so scroll events are identified as changes to the horizontal or
- // vertical start value.
- if (eventName.equals(ViewportRanges.STARTRES))
- {
- if (av.getWrapAlignment())
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
{
fastPaintWrapped(scrollX);
}
{
fastPaintWrapped(scrollX);
}
- else
- {
- fastPaint(scrollX, 0);
- }
- // bizarrely, we only need to scroll on the x value here as fastpaint
- // copies the full height of the image anyway. Passing in the y value
- // causes nasty repaint artefacts, which only disappear on a full
- // repaint.
}
}
{
ViewportRanges ranges = av.getRanges();
- // if (Math.abs(scrollX) > ranges.getViewportWidth())
- // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
- if (true)
+ if (Math.abs(scrollX) > ranges.getViewportWidth())
{
/*
* shift of more than one view width is
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
if (av.hasHiddenColumns())
{
displayColumn = alignment.getHiddenColumns()
- .findColumnPosition(displayColumn);
+ .absoluteToVisibleColumn(displayColumn);
}
/*
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
return res;
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
- // TODO: once JAL-2759 is ready, change this loop to something more
- // efficient
- while (!hidden.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
- && dx != 0)
+ if (!hidden.isVisible(seqCanvas.cursorX))
{
- seqCanvas.cursorX += dx;
+ int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
+ int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+ if (region != null) // just in case
+ {
+ if (dx == 1)
+ {
+ // moving right
+ seqCanvas.cursorX = region[1] + 1;
+ }
+ else if (dx == -1)
+ {
+ // moving left
+ seqCanvas.cursorX = region[0] - 1;
+ }
+ }
+ seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
}
if (seqCanvas.cursorX >= maxWidth
{
// scrollToWrappedVisible expects x-value to have hidden cols subtracted
int x = av.getAlignment().getHiddenColumns()
- .findColumnPosition(seqCanvas.cursorX);
+ .absoluteToVisibleColumn(seqCanvas.cursorX);
av.getRanges().scrollToWrappedVisible(x);
}
else
{
fixedColumns = true;
int y1 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryLeft(startres);
+ .getNextHiddenBoundary(true, startres);
int y2 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryRight(startres);
+ .getNextHiddenBoundary(false, startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
if (sg.getSize() == av.getAlignment().getHeight())
{
if ((av.hasHiddenColumns() && startres < av.getAlignment()
- .getHiddenColumns().getHiddenBoundaryRight(startres)))
+ .getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
{
endEditing();
return;
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
if (e.isShiftDown())
{
av.getRanges().scrollUp(false);
}
}
- else
+ else if (wheelRotation < 0)
{
if (e.isShiftDown())
{
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
- boolean vischange = stretchGroup.recalcConservation(true);
+ boolean vischange = stretchGroup.recalcAnnotations(true);
updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
&& afterDrag;
if (stretchGroup.cs != null)
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.api.SplitContainerI;
import jalview.datamodel.AlignmentI;
import jalview.jbgui.GAlignFrame;
topFrame.alignPanel.adjustAnnotationHeight();
bottomFrame.alignPanel.adjustAnnotationHeight();
- final AlignViewport topViewport = topFrame.viewport;
- final AlignViewport bottomViewport = bottomFrame.viewport;
+ final AlignViewportI topViewport = topFrame.viewport;
+ final AlignViewportI bottomViewport = bottomFrame.viewport;
final AlignmentI topAlignment = topViewport.getAlignment();
final AlignmentI bottomAlignment = bottomViewport.getAlignment();
boolean topAnnotations = topViewport.isShowAnnotation();
package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
/**
}
/**
+ * select structures for viewing by their PDB IDs
+ *
+ * @param pdbids
+ * @return true if structures were found and marked as selected
+ */
+ public boolean selectStructure(String... pdbids)
+ {
+ boolean found = false;
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
+
+ if (restable == null)
+ {
+ // can't select (enter PDB ID, or load file - need to also select which
+ // sequence to associate with)
+ return false;
+ }
+
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+ for (int r = 0; r < restable.getRowCount(); r++)
+ {
+ for (int p = 0; p < pdbids.length; p++)
+ {
+ if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+ .equalsIgnoreCase(pdbids[p]))
+ {
+ restable.setRowSelectionInterval(r, r);
+ found = true;
+ }
+ }
+ }
+ return found;
+ }
+ /**
* Handles action event for btn_ok
*/
@Override
public void ok_ActionPerformed()
{
+ showStructures(false);
+ }
+
+ /**
+ * structure viewer opened by this dialog, or null
+ */
+ private StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
- new Thread(new Runnable()
+ Runnable viewStruc = new Runnable()
{
@Override
public void run()
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : tbl_local_pdb;
+
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = getResultTable().getColumn("PDB Id")
+ int pdbIdColIndex = restable.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
.getModelIndex();
- int[] selectedRows = getResultTable().getSelectedRows();
+ int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- String pdbIdStr = getResultTable()
+ String pdbIdStr = restable
.getValueAt(row, pdbIdColIndex).toString();
- SequenceI selectedSeq = (SequenceI) getResultTable()
+ SequenceI selectedSeq = (SequenceI) restable
.getValueAt(row, refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[]
{ selectedSequence });
}
DataSourceType.FILE, selectedSequence, true,
Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ sViewer = launchStructureViewer(
+ ssm, new PDBEntry[]
+ { fileEntry }, ap,
new SequenceI[]
{ selectedSequence });
}
- closeAction(preferredHeight);
- mainFrame.dispose();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
}
- }).start();
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
+ {
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
+ {
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
+ {
+
+ }
+ }
+ }
}
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
return foundEntry;
}
- private void launchStructureViewer(StructureSelectionManager ssm,
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm,
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
setProgressBar(null, progressId);
+ return sViewer;
}
/**
{
return progressBar.operationInProgress();
}
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
}
new PDBEntry[seqsForPdbs.size()]);
SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
new SequenceI[seqsForPdbs.size()][]);
- JalviewStructureDisplayI sview = null;
+
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(ap, pdbsForFile, theSeqs);
private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
SequenceI[] seqsForPdbs, AlignmentPanel ap)
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
if (pdbs == null || pdbs.length == 0)
{
return null;
ap);
}
+ JalviewStructureDisplayI sview = null;
+
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
ViewerType viewerType = getViewerType();
- JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
final boolean viewerColouring = viewerData.isColourByViewer();
- JalviewStructureDisplayI sview = null;
switch (type)
{
case JMOL:
return sview;
}
+ public boolean isBusy()
+ {
+ if (sview != null)
+ {
+ if (!sview.hasMapping())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
}
import jalview.jbgui.GStructureViewer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
protected boolean alignAddedStructures = false;
- protected boolean _started = false;
+ protected volatile boolean _started = false;
- protected boolean addingStructures = false;
+ protected volatile boolean addingStructures = false;
protected Thread worker = null;
protected JMenu viewSelectionMenu;
/**
+ * set after sequence colouring has been applied for this structure viewer.
+ * used to determine if the final sequence/structure mapping has been
+ * determined
+ */
+ protected volatile boolean seqColoursApplied = false;
+
+ /**
* Default constructor
*/
public StructureViewerBase()
{
binding.colourBySequence(ap);
}
+ seqColoursApplied = true;
}
}
seqColour_actionPerformed(null);
}
}
+
+ @Override
+ public boolean hasMapping()
+ {
+ if (worker != null && (addingStructures || _started))
+ {
+ return false;
+ }
+ if (getBinding() == null)
+ {
+ if (_aps == null || _aps.size() == 0)
+ {
+ // viewer has been closed, but we did at some point run.
+ return true;
+ }
+ return false;
+ }
+ String[] pdbids = getBinding().getStructureFiles();
+ if (pdbids == null)
+ {
+ return false;
+ }
+ int p=0;
+ for (String pdbid:pdbids) {
+ StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+ if (sm!=null && sm.length>0 && sm[0]!=null) {
+ p++;
+ }
+ }
+ // only return true if there is a mapping for every structure file we have loaded
+ if (p == 0 || p != pdbids.length)
+ {
+ return false;
+ }
+ // and that coloring has been applied
+ return seqColoursApplied;
+ }
+
}
}
else
{
- // int[] intervals = colsel.getVisibleContigs(
- // seqsel.getStartRes(), seqsel.getEndRes() + 1);
- int[] intervals = hidden.getVisibleContigs(
- seqsel.getStartRes(), seqsel.getEndRes() + 1);
- for (int iv = 0; iv < intervals.length; iv += 2)
+ Iterator<int[]> intervals = hidden
+ .getVisContigsIterator(seqsel.getStartRes(),
+ seqsel.getEndRes() + 1, false);
+ while (intervals.hasNext())
{
+ int[] region = intervals.next();
Seg s = new Seg();
- s.setStart(intervals[iv] + 1); // vamsas indices begin at
- // 1, not zero.
- s.setEnd(intervals[iv + 1] + 1);
+ s.setStart(region[0] + 1); // vamsas indices begin at 1,
+ // not zero.
+ s.setEnd(region[1] + 1);
s.setInclusive(true);
range.addSeg(s);
}
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
-import net.miginfocom.swing.MigLayout;
-
import compbio.metadata.Argument;
import compbio.metadata.Option;
import compbio.metadata.Parameter;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
+import net.miginfocom.swing.MigLayout;
/**
* job parameter editing/browsing dialog box. User can browse existing settings
this(service, null);
}
+ public WsJobParameters(JFrame parent, ParamDatastoreI store,
+ WsParamSetI preset,
+ List<ArgumentI> args)
+ {
+ super();
+ jbInit();
+ this.paramStore = store;
+ this.service = null;
+ // argSetModified(false);
+ // populate parameter table
+ init(preset, args);
+ // display in new JFrame attached to parent.
+ validate();
+ }
+
public WsJobParameters(Jws2Instance service, WsParamSetI preset)
{
this(null, service, preset, null);
{
frame = new JDialog(Desktop.instance, true);
+ if (service != null)
+ {
+ frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+ new String[]
+ { service.getActionText() }));
+ }
- frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
- new String[]
- { service.getActionText() }));
Rectangle deskr = Desktop.instance.getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(
// null;
}
+ init(p, jobArgset);
+
+ }
+
+ void init(WsParamSetI p, List<ArgumentI> jobArgset)
+ {
Hashtable exnames = new Hashtable();
for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
{
}
}
settingDialog = false;
-
}
@SuppressWarnings("unchecked")
int p = 0;
if (args.length > 0)
{
- Vector<String> services = new Vector<String>();
+ Vector<String> services = new Vector<>();
services.addElement(args[p++]);
Jws2Discoverer.getDiscoverer().setServiceUrls(services);
}
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- System.out.println("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ // System.out.println("Item state changed for " + setname
+ // + " (handling ? " + !settingDialog + ")");
if (settingDialog)
{
// ignore event
--- /dev/null
+package jalview.hmmer;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SplitFrame;
+import jalview.io.DataSourceType;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
+public class HMMAlign extends HmmerCommand
+{
+ static final String HMMALIGN = "hmmalign";
+
+ static final String ARG_TRIM = "--trim";
+
+ private final AlignmentI dataset;
+
+ /**
+ * Constructor for the HMMAlignThread
+ *
+ * @param af
+ * @param args
+ */
+ public HMMAlign(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ if (alignment.getDataset() != null)
+ {
+ dataset = alignment.getDataset();
+ }
+ else
+ {
+ dataset = null;
+ }
+ }
+
+ /**
+ * Runs the HMMAlignThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame (if true). The command is executed
+ * for each segment of the alignment. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ HiddenMarkovModel hmm = af.getSelectedHMM();
+ if (hmm == null)
+ {
+ System.err.println("Can't run hmmalign as no HMM profile selected");
+ return;
+ }
+
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ msgId);
+
+ AlignmentView msa = af.gatherSequencesForAlignment();
+ SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());
+
+ List<AlignmentOrder> allOrders = new ArrayList<>();
+
+ SequenceI[][] allResults = new SequenceI[subAlignments.length][];
+ int job = 0;
+ for (SequenceI[] seqs : subAlignments)
+ {
+ Hashtable sequencesHash = stashSequences(seqs);
+ try
+ {
+ File modelFile = createTempFile("hmm", ".hmm");
+ File alignmentFile = createTempFile("output", ".sto");
+ File resultFile = createTempFile("input", ".sto");
+
+ exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
+ exportHmm(hmm, modelFile.getAbsoluteFile());
+
+ boolean ran = runCommand(modelFile, alignmentFile, resultFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
+
+ SequenceI[] result = importData(resultFile, allOrders);
+ recoverSequences(sequencesHash, result);
+ allResults[job] = result;
+ modelFile.delete();
+ alignmentFile.delete();
+ resultFile.delete();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ job++;
+ }
+
+ String title = "hmmalign to " + hmm.getConsensusSequence().getName();
+ displayResults(allResults, allOrders, msa, title);
+
+ af.setProgressBar("", msgId);
+ }
+
+ /**
+ * Executes the hmmalign command and returns true if successful, false if an
+ * error is detected
+ *
+ * @param modelFile
+ * the HMM to align to
+ * @param alignmentFile
+ * the sequences to align
+ * @param resultFile
+ * the file to hold the results of alignment
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File modelFile, File alignmentFile,
+ File resultFile) throws IOException
+ {
+ String command = getCommandPath(HMMALIGN);
+ if (command == null)
+ {
+ return false;
+ }
+ List<String> args = new ArrayList<>();
+ args.add(command);
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.trim_termini").equals(name))
+ {
+ args.add(ARG_TRIM);
+ }
+ }
+ }
+ args.add("-o");
+ args.add(resultFile.getAbsolutePath());
+ args.add(modelFile.getAbsolutePath());
+ args.add(alignmentFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the data from the file holding the output of hmmalign
+ *
+ * @param resultFile
+ * @param allOrders
+ * a list of alignment orders to add to
+ *
+ * @return
+ * @throws IOException
+ */
+ private SequenceI[] importData(File resultFile,
+ List<AlignmentOrder> allOrders) throws IOException
+ {
+ StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ SequenceI[] result = file.getSeqsAsArray();
+ AlignmentOrder msaorder = new AlignmentOrder(result);
+ AlignmentSorter.recoverOrder(result);
+ allOrders.add(msaorder);
+
+ return result;
+ }
+
+ /**
+ * Displays the results of all 'jobs' in a new frame
+ *
+ * @param allResults
+ *
+ * @param allOrders
+ * @param msa
+ * @param title
+ */
+ private void displayResults(SequenceI[][] allResults,
+ List<AlignmentOrder> allOrders, AlignmentView msa, String title)
+ {
+ AlignmentOrder[] arrOrders = allOrders
+ .toArray(new AlignmentOrder[allOrders.size()]);
+ Object[] newview = msa.getUpdatedView(allResults, arrOrders,
+ alignment.getGapCharacter());
+ SequenceI[] seqs = (SequenceI[]) newview[0];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
+ Alignment al = new Alignment(seqs);
+ al.setProperty("Alignment Program", "hmmalign");
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ /*
+ * hack to ensure hmm set on alignment
+ */
+ if (al.getSequenceAt(0).isHMMConsensusSequence())
+ {
+ al.setHmmConsensus(al.getSequenceAt(0));
+ }
+
+ displayInNewFrame(al, allOrders, hidden, title);
+ }
+
+ /**
+ * Displays the results in a new frame
+ *
+ * @param al
+ * The alignment containing the results
+ * @param alorders
+ * The order of the sequences in the alignment on which the jobs were
+ * run
+ * @param hidden
+ * Hidden columns in the previous alignment
+ * @param title
+ */
+ private void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, HiddenColumns hidden, String title)
+ {
+ AlignFrame alignFrame = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.setTitle(title);
+
+ FeatureRendererSettings featureSettings = af.getFeatureRenderer()
+ .getSettings();
+ // initialise with same renderer settings as in parent alignframe.
+ alignFrame.getFeatureRenderer().transferSettings(featureSettings);
+
+ addSortByMenuItems(alignFrame, alorders);
+
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = this.af;
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complement.getDataset());
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ alignFrame.setTitle(this.af.getTitle());
+ AlignFrame af2 = new AlignFrame(copyComplement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af2.setTitle(complementTitle);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(
+ al.isNucleotide() ? alignFrame : af2, al.isNucleotide() ? af2 : alignFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
+ }
+ }
+
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(alignFrame, alignFrame.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Adds sort order options to the AlignFrame menus
+ *
+ * @param alignFrame
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame alignFrame,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ alignFrame.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
+ }
+ else
+ {
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ alignFrame.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+ alorders.get(i));
+ }
+ }
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * A class that runs the hmmbuild command as a separate process.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class HMMBuild extends HmmerCommand
+{
+ static final String ARG_AMINO = "--amino";
+
+ static final String ARG_DNA = "--dna";
+
+ static final String ARG_RNA = "--rna";
+
+ /**
+ * Constructor
+ *
+ * @param alignFrame
+ * @param args
+ */
+ public HMMBuild(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ super(alignFrame, args);
+ }
+
+ /**
+ * Builds a HMM from an alignment (and/or groups), then imports and adds it to
+ * the alignment (and/or groups). Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ if (params == null || params.isEmpty())
+ {
+ Cache.log.error("No parameters to HMMBuild!|");
+ return;
+ }
+
+ long msgID = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ msgID);
+
+ AlignViewportI viewport = af.getViewport();
+ try
+ {
+ /*
+ * run hmmbuild for alignment and/or groups as selected
+ */
+ List<AnnotatedCollectionI> runBuildFor = parseParameters(viewport);
+
+ for (AnnotatedCollectionI grp : runBuildFor)
+ {
+ runHMMBuild(grp);
+ }
+ } finally
+ {
+ af.setProgressBar("", msgID);
+ viewport.alignmentChanged(af.alignPanel);
+ af.buildColourMenu(); // to enable HMMER colour schemes
+ }
+ }
+
+ /**
+ * Scans the parameters to determine whether to run hmmmbuild for the whole
+ * alignment or specified subgroup(s) or both
+ *
+ * @param viewport
+ * @return
+ */
+ protected List<AnnotatedCollectionI> parseParameters(
+ AlignViewportI viewport)
+ {
+ List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
+ {
+ String value = arg.getValue();
+ if (MessageManager.getString("label.alignment").equals(value))
+ {
+ runBuildFor.add(alignment);
+ }
+ else if (MessageManager.getString("label.groups_and_alignment")
+ .equals(value))
+ {
+ runBuildFor.add(alignment);
+ runBuildFor.addAll(viewport.getAlignment().getGroups());
+ }
+ else if (MessageManager.getString("label.groups").equals(value))
+ {
+ runBuildFor.addAll(viewport.getAlignment().getGroups());
+ }
+ else if (MessageManager.getString("label.selected_group")
+ .equals(value))
+ {
+ runBuildFor.add(viewport.getSelectionGroup());
+ }
+ }
+ else if (MessageManager.getString("label.use_reference")
+ .equals(name))
+ {
+ // todo disable this option if no RF annotation on alignment
+ if (!af.getViewport().hasReferenceAnnotation())
+ {
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .getString("warn.no_reference_annotation"));
+ // return;
+ }
+ }
+ }
+ return runBuildFor;
+ }
+
+ /**
+ * Runs hmmbuild on the given sequences (alignment or group)
+ *
+ * @param grp
+ */
+ private void runHMMBuild(AnnotatedCollectionI ac)
+ {
+ File hmmFile = null;
+ File alignmentFile = null;
+ try
+ {
+ hmmFile = createTempFile("hmm", ".hmm");
+ alignmentFile = createTempFile("output", ".sto");
+
+ if (ac instanceof Alignment)
+ {
+ AlignmentI al = (Alignment) ac;
+ // todo pad gaps in an unaligned SequenceGroup as well?
+ if (!al.isAligned())
+ {
+ al.padGaps();
+ }
+ }
+
+ deleteHmmSequences(ac);
+
+ List<SequenceI> copy = new ArrayList<>();
+ if (ac instanceof Alignment)
+ {
+ copy.addAll(ac.getSequences());
+ }
+ else
+ {
+ SequenceI[] sel = ((SequenceGroup) ac)
+ .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+ for (SequenceI seq : sel)
+ {
+ copy.add(seq);
+ }
+ }
+
+ SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
+ Hashtable sequencesHash = stashSequences(copyArray);
+
+ exportStockholm(copyArray, alignmentFile, ac);
+
+ recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
+
+ boolean ran = runCommand(alignmentFile, hmmFile, ac);
+ if (!ran)
+ {
+ return;
+ }
+ importData(hmmFile, ac);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ if (hmmFile != null)
+ {
+ hmmFile.delete();
+ }
+ if (alignmentFile != null)
+ {
+ alignmentFile.delete();
+ }
+ }
+ }
+
+ /**
+ * A helper method that deletes any HMM consensus sequence from the given
+ * collection, and from the parent alignment if <code>ac</code> is a subgroup
+ *
+ * @param ac
+ */
+ void deleteHmmSequences(AnnotatedCollectionI ac)
+ {
+ SequenceI hmmSeq = ac.getHmmConsensus();
+ if (hmmSeq != null)
+ {
+ if (ac instanceof SequenceGroup)
+ {
+ ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
+ AnnotatedCollectionI context = ac.getContext();
+ if (context != null && context instanceof AlignmentI)
+ {
+ ((AlignmentI) context).deleteSequence(hmmSeq);
+ }
+ }
+ else
+ {
+ ((AlignmentI) ac).deleteSequence(hmmSeq);
+ }
+ }
+ }
+
+ /**
+ * Constructs and executes the hmmbuild command as a separate process
+ *
+ * @param sequencesFile
+ * the alignment from which the HMM is built
+ * @param hmmFile
+ * the output file to which the HMM is written
+ * @param group
+ * alignment or group for which the hmm is generated
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File sequencesFile, File hmmFile,
+ AnnotatedCollectionI group) throws IOException
+ {
+ String cmd = getCommandPath(HMMBUILD);
+ if (cmd == null)
+ {
+ return false; // executable not found
+ }
+ List<String> args = new ArrayList<>();
+ args.add(cmd);
+
+ /*
+ * HMM name (will be given to consensus sequence) is
+ * - as specified by an input parameter if set
+ * - else group name with _HMM appended (if for a group)
+ * - else align frame title with _HMM appended (if title is not too long)
+ * - else "Alignment_HMM"
+ */
+ String name = "";
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String argName = arg.getName();
+ switch (argName)
+ {
+ case "HMM Name":
+ name = arg.getValue().trim();
+ break;
+ case "Use Reference Annotation":
+ args.add("--hand");
+ break;
+ }
+ }
+ }
+
+ if (group instanceof SequenceGroup)
+ {
+ name = ((SequenceGroup) group).getName() + "_HMM";
+ }
+
+ if ("".equals(name))
+ {
+ if (af != null && af.getTitle().length() < 15)
+ {
+ name = af.getTitle();
+ }
+ else
+ {
+ name = "Alignment_HMM";
+ }
+ }
+
+ args.add("-n");
+ args.add(name.replace(' ', '_'));
+ if (!alignment.isNucleotide())
+ {
+ args.add(ARG_AMINO); // TODO check for rna
+ }
+ else
+ {
+ args.add(ARG_DNA);
+ }
+
+ args.add(hmmFile.getAbsolutePath());
+ args.add(sequencesFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
+ * sequence (with attached HMM profile) as the first sequence in the alignment
+ * or group for which it was generated
+ *
+ * @param hmmFile
+ * @param ac
+ * (optional) the group for which the hmm was generated
+ * @throws IOException
+ */
+ private void importData(File hmmFile, AnnotatedCollectionI ac)
+ throws IOException
+ {
+ HMMFile file = new HMMFile(
+ new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
+ SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+ if (ac instanceof SequenceGroup)
+ {
+ SequenceGroup grp = (SequenceGroup) ac;
+ char gapChar = alignment.getGapCharacter();
+ hmmSeq.insertCharAt(0, ac.getStartRes(), gapChar);
+ hmmSeq.insertCharAt(ac.getEndRes() + 1,
+ alignment.getWidth() - ac.getEndRes() - 1, gapChar);
+ SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
+ int topIndex = alignment.findIndex(topSeq);
+ alignment.insertSequenceAt(topIndex, hmmSeq);
+ ac.setSeqrep(hmmSeq);
+ grp.addSequence(hmmSeq, false);
+ grp.setHmmConsensus(hmmSeq);
+ }
+ else
+ {
+ alignment.insertSequenceAt(0, hmmSeq);
+ alignment.setHmmConsensus(hmmSeq);
+ }
+
+ if (af.getSelectedHMM() == null)
+ {
+ af.setSelectedHMMSequence(hmmSeq);
+ }
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.LogarithmicParameter;
+import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Scanner;
+
+public final class HMMERParamStore implements ParamDatastoreI
+{
+ private static final String HMMBUILD = "hmmbuild";
+
+ private static final String HMMALIGN = "hmmalign";
+
+ private static final String HMMSEARCH = "hmmsearch";
+
+ String name;
+
+ List<WsParamSetI> presets = new ArrayList<>();
+
+ private HMMERParamStore(String nam)
+ {
+ this.name = nam;
+ }
+
+ public static HMMERParamStore forBuild()
+ {
+ return new HMMERParamStore(HMMBUILD);
+ }
+
+ public static HMMERParamStore forAlign()
+ {
+ return new HMMERParamStore(HMMALIGN);
+ }
+
+ public static HMMERParamStore forSearch()
+ {
+ return new HMMERParamStore(HMMSEARCH);
+ }
+
+ @Override
+ public List<WsParamSetI> getPresets()
+ {
+ return presets;
+ }
+
+ @Override
+ public WsParamSetI getPreset(String nam)
+ {
+ return null;
+ }
+
+ @Override
+ public List<ArgumentI> getServiceParameters()
+ {
+ List<ArgumentI> args = new ArrayList<>();
+ switch (name)
+ {
+ case HMMSEARCH:
+ getHMMSearchParams(args);
+ break;
+ case HMMALIGN:
+ getHMMAlignParams(args);
+ break;
+ case HMMBUILD:
+ getHMMBuildParams(args);
+ break;
+ default:
+ }
+
+ return args;
+ }
+
+ private void getHMMSearchParams(List<ArgumentI> args)
+ {
+ args.add(new IntegerParameter(
+ MessageManager.getString("label.number_of_results"),
+ MessageManager.getString("label.number_of_results_desc"), true,
+ 100, 0, 100000));
+ String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ if (names != null && !names.isEmpty())
+ {
+ Collection<String> databases = new ArrayList<>();
+ databases.add(MessageManager.getString("label.this_alignment"));
+ Scanner nameScanner = new Scanner(names);
+
+ if (nameScanner.hasNext())
+ {
+ while (nameScanner.hasNext())
+ {
+ String next = nameScanner.next();
+ if ("null".equals(next))
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+ }
+ else
+ {
+ databases.add(next);
+ }
+ }
+ }
+ nameScanner.close();
+ args.add(new Option(MessageManager.getString("label.database"),
+ MessageManager.getString("label.database_for_hmmsearch"),
+ true, MessageManager.getString("label.this_alignment"),
+ MessageManager.getString("label.this_alignment"), databases,
+ null));
+ }
+ args.add(new BooleanOption(
+ MessageManager.getString("label.auto_align_seqs"),
+ MessageManager.getString("label.auto_align_seqs_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_accessions"),
+ MessageManager.getString("label.use_accessions_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), false,
+ false, true, null));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.seq_e_value"),
+ MessageManager.getString("label.seq_e_value_desc"), false, -3d,
+ -37.92977945, 1d, 10d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.seq_score"),
+ MessageManager.getString("label.seq_score_desc"), false,
+ 0d, 0d, 10000d));
+ */
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.dom_e_value_desc"),
+ MessageManager.getString("label.dom_e_value_desc"), false, -3d,
+ -37.92977945, 1d, 10d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.dom_score"),
+ MessageManager.getString("label.dom_score_desc"), false, 0d,
+ 0d,
+ 10000d));
+ */
+ }
+
+ private void getHMMAlignParams(List<ArgumentI> args)
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"),
+ false, false, true, null));
+ }
+
+ private void getHMMBuildParams(List<ArgumentI> args)
+ {
+ args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
+ MessageManager.getString("label.hmm_name_desc"), true, ""));
+ // todo only enable Use Reference Annotation if RF is present
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_reference"),
+ MessageManager.getString("label.use_reference_desc"), true,
+ true, true, null));
+
+ Collection<String> options = new ArrayList<>();
+ options.add(MessageManager.getString("label.alignment"));
+ options.add(MessageManager.getString("label.groups_and_alignment"));
+ options.add(MessageManager.getString("label.groups"));
+ options.add(MessageManager.getString("label.selected_group"));
+
+ args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+ MessageManager.getString("label.hmmbuild_for_desc"), true,
+ MessageManager.getString("label.alignment"),
+ MessageManager.getString("label.alignment"), options, null));
+ }
+
+ @Override
+ public boolean presetExists(String forName)
+ {
+ return false;
+ }
+
+ @Override
+ public void deletePreset(String forName)
+ {
+ }
+
+ @Override
+ public void storePreset(String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ }
+
+ @Override
+ public void updatePreset(String oldName, String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ }
+
+ @Override
+ public WsParamSetI parseServiceParameterFile(String forName,
+ String description, String[] serviceURL, String parameters)
+ throws IOException
+ {
+ return null;
+ }
+
+ @Override
+ public String generateServiceParameterFile(WsParamSetI pset)
+ throws IOException
+ {
+ return null;
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.List;
+
+public class HMMERPreset implements WsParamSetI
+{
+
+ @Override
+ public String getName()
+ {
+ return null;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return null;
+ }
+
+ @Override
+ public String[] getApplicableUrls()
+ {
+ return null;
+ }
+
+ @Override
+ public String getSourceFile()
+ {
+ return null;
+ }
+
+ @Override
+ public void setSourceFile(String newfile)
+ {
+ }
+
+ @Override
+ public boolean isModifiable()
+ {
+ return false;
+ }
+
+ @Override
+ public List<ArgumentI> getArguments()
+ {
+ return null;
+ }
+
+ @Override
+ public void setArguments(List<ArgumentI> args)
+ {
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.BooleanOption;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import javax.swing.JOptionPane;
+
+public class HMMSearch extends HmmerCommand
+{
+ static final String HMMSEARCH = "hmmsearch";
+
+ boolean realign = false;
+
+ boolean trim = false;
+
+ int seqsToReturn = Integer.MAX_VALUE;
+
+ SequenceI[] seqs;
+
+ /**
+ * Constructor for the HMMSearchThread
+ *
+ * @param af
+ */
+ public HMMSearch(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ }
+
+ /**
+ * Runs the HMMSearchThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ HiddenMarkovModel hmm = af.getSelectedHMM();
+ if (hmm == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return;
+ }
+
+ SequenceI hmmSeq = af.getSelectedHMMSequence();
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ msgId);
+
+ try
+ {
+ File hmmFile = createTempFile("hmm", ".hmm");
+ File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
+ File searchOutputFile = createTempFile("searchOutput", ".sto");
+
+ exportHmm(hmm, hmmFile.getAbsoluteFile());
+
+ boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmsearch_failed"));
+ return;
+ }
+
+ importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
+ // TODO make realignment of search results a step at this level
+ // and make it conditional on this.realign
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ finally
+ {
+ af.setProgressBar("", msgId);
+ }
+ }
+
+ /**
+ * Executes an hmmsearch with the given hmm as input. The database to be
+ * searched is a local file as specified by the 'Database' parameter, or the
+ * current alignment (written to file) if none is specified.
+ *
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+ File hmmFile) throws IOException
+ {
+ String command = getCommandPath(HMMSEARCH);
+ if (command == null)
+ {
+ return false;
+ }
+
+ List<String> args = new ArrayList<>();
+ args.add(command);
+ args.add("-o");
+ args.add(searchOutputFile.getAbsolutePath());
+ args.add("-A");
+ args.add(hitsAlignmentFile.getAbsolutePath());
+
+ boolean dbFound = false;
+ String dbPath = "";
+ File databaseFile = null;
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.number_of_results")
+ .equals(name))
+ {
+ seqsToReturn = Integer.parseInt(arg.getValue());
+ }
+ else if (MessageManager.getString("label.auto_align_seqs")
+ .equals(name))
+ {
+ realign = true; // TODO: not used
+ }
+ else if (MessageManager.getString("label.use_accessions")
+ .equals(name))
+ {
+ args.add("--acc");
+ }
+ else if (MessageManager.getString("label.seq_e_value").equals(name))
+ {
+ args.add("--incE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.seq_score").equals(name))
+ {
+ args.add("-incT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_e_value_desc")
+ .equals(name))
+ {
+ args.add("--incdomE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_score").equals(name))
+ {
+ args.add("--incdomT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.trim_termini")
+ .equals(name))
+ {
+ trim = true;
+ }
+ else if (MessageManager.getString("label.database").equals(name))
+ {
+ dbFound = true;
+ dbPath = arg.getValue();
+ if (!MessageManager.getString("label.this_alignment")
+ .equals(dbPath))
+ {
+ databaseFile = new File(dbPath);
+ }
+ }
+ }
+ }
+
+ if (!dbFound || MessageManager.getString("label.this_alignment")
+ .equals(dbPath))
+ {
+ /*
+ * no external database specified for search, so
+ * export current alignment as 'database' to search
+ */
+ databaseFile = createTempFile("database", ".sto");
+ AlignmentI al = af.getViewport().getAlignment();
+ AlignmentI copy = new Alignment(al);
+ SequenceI hmms = copy.getHmmConsensus();
+ if (hmms != null)
+ {
+ copy.deleteSequence(hmms);
+ }
+ exportStockholm(copy.getSequencesArray(), databaseFile, null);
+ // StockholmFile stoFile = new StockholmFile(copy);
+ // stoFile.setSeqs(copy.getSequencesArray());
+ // String alignmentString = stoFile.print();
+ // PrintWriter writer = new PrintWriter(databaseFile);
+ // writer.print(alignmentString);
+ // writer.close();
+ }
+
+ args.add(hmmFile.getAbsolutePath());
+ args.add(databaseFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the data from the temporary file to which the output of hmmsearch
+ * is directed.
+ *
+ * @param hmmSeq
+ */
+ private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
+ File hmmTemp, File searchOutputFile)
+ throws IOException, InterruptedException
+ {
+ BufferedReader br = new BufferedReader(
+ new FileReader(inputAlignmentTemp));
+ try
+ {
+ if (br.readLine() == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("label.no_sequences_found"));
+ return;
+ }
+ StockholmFile file = new StockholmFile(new FileParse(
+ inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+ seqs = file.getSeqsAsArray();
+
+ readTable(searchOutputFile);
+
+ int seqCount = Math.min(seqs.length, seqsToReturn);
+ SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+ hmmAndSeqs[0] = hmmSeq;
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
+
+ AlignmentI alignment = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(alignment, 1, 1);
+ frame.setSelectedHMMSequence(hmmSeq);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ if (trim)
+ {
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
+ }
+ HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+ hmmalign.run();
+ frame = null;
+ hmmTemp.delete();
+ inputAlignmentTemp.delete();
+ searchOutputFile.delete();
+ } finally
+ {
+ if (br != null)
+ {
+ br.close();
+ }
+ }
+ }
+
+ void readTable(File inputTableTemp) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+ String line = "";
+ while (!line.startsWith("Query:"))
+ {
+ line = br.readLine();
+ }
+ for (int i = 0; i < 5; i++)
+ {
+ line = br.readLine();
+ }
+
+ int index = 0;
+ while (!" ------ inclusion threshold ------".equals(line)
+ && !"".equals(line))
+ {
+ Scanner scanner = new Scanner(line);
+
+ String str = scanner.next(); // full sequence eValue score
+ float eValue = Float.parseFloat(str);
+ int seqLength = seqs[index].getLength();
+ Annotation[] annots = new Annotation[seqLength];
+ for (int j = 0; j < seqLength; j++)
+ {
+ annots[j] = new Annotation(eValue);
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
+ "Score", annots);
+ annot.setScore(Double.parseDouble(str));
+ annot.setSequenceRef(seqs[index]);
+ seqs[index].addAlignmentAnnotation(annot);
+
+ scanner.close();
+ line = br.readLine();
+ index++;
+ }
+
+ br.close();
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * Base class for hmmbuild, hmmalign and hmmsearch
+ *
+ * @author TZVanaalten
+ *
+ */
+public abstract class HmmerCommand implements Runnable
+{
+ public static final String HMMBUILD = "hmmbuild";
+
+ protected final AlignFrame af;
+
+ protected final AlignmentI alignment;
+
+ protected final List<ArgumentI> params;
+
+ /**
+ * Constructor
+ *
+ * @param alignFrame
+ * @param args
+ */
+ public HmmerCommand(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ af = alignFrame;
+ alignment = af.getViewport().getAlignment();
+ params = args;
+ }
+
+ /**
+ * Answers true if preference HMMER_PATH is set, and its value is the path to
+ * a directory that contains an executable <code>hmmbuild</code> or
+ * <code>hmmbuild.exe</code>, else false
+ *
+ * @return
+ */
+ public static boolean isHmmerAvailable()
+ {
+ File exec = getExecutable(HMMBUILD, Cache.getProperty(Preferences.HMMER_PATH));
+ return exec != null;
+ }
+
+ /**
+ * Uniquifies the sequences when exporting and stores their details in a
+ * hashtable
+ *
+ * @param seqs
+ */
+ protected Hashtable stashSequences(SequenceI[] seqs)
+ {
+ return SeqsetUtils.uniquify(seqs, true);
+ }
+
+ /**
+ * Restores the sequence data lost by uniquifying
+ *
+ * @param hashtable
+ * @param seqs
+ */
+ protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+ {
+ SeqsetUtils.deuniquify(hashtable, seqs);
+ }
+
+ /**
+ * Runs a command as a separate process and waits for it to complete. Answers
+ * true if the process return status is zero, else false.
+ *
+ * @param command
+ * the executable command and any arguments to it
+ * @throws IOException
+ */
+ public boolean runCommand(List<String> command)
+ throws IOException
+ {
+ try
+ {
+ ProcessBuilder pb = new ProcessBuilder(command);
+ pb.redirectErrorStream(true); // merge syserr to sysout
+ final Process p = pb.start();
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BufferedReader input = new BufferedReader(
+ new InputStreamReader(p.getInputStream()));
+ try
+ {
+ String line = input.readLine();
+ while (line != null)
+ {
+ System.out.println(line);
+ line = input.readLine();
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }).start();
+
+ p.waitFor();
+ return p.exitValue() == 0; // 0 is success, by convention
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ return false;
+ }
+ }
+
+ /**
+ * Exports an alignment, and reference (RF) annotation if present, to the
+ * specified file, in Stockholm format
+ *
+ * @param seqs
+ * @param toFile
+ * @param annotated
+ * @throws IOException
+ */
+ public void exportStockholm(SequenceI[] seqs, File toFile,
+ AnnotatedCollectionI annotated) throws IOException
+ {
+ if (seqs == null)
+ {
+ return;
+ }
+ AlignmentI newAl = new Alignment(seqs);
+ if (!newAl.isAligned())
+ {
+ newAl.padGaps();
+ }
+
+ if (toFile != null && annotated != null)
+ {
+ AlignmentAnnotation[] annots = annotated.getAlignmentAnnotation();
+ if (annots != null)
+ {
+ for (AlignmentAnnotation annot : annots)
+ {
+ if (annot.label.contains("Reference") || "RF".equals(annot.label))
+ {
+ AlignmentAnnotation newRF;
+ if (annot.annotations.length > newAl.getWidth())
+ {
+ Annotation[] rfAnnots = new Annotation[newAl.getWidth()];
+ System.arraycopy(annot.annotations, 0, rfAnnots, 0,
+ rfAnnots.length);
+ newRF = new AlignmentAnnotation("RF", "Reference Positions",
+ rfAnnots);
+ }
+ else
+ {
+ newRF = new AlignmentAnnotation(annot);
+ }
+ newAl.addAnnotation(newRF);
+ }
+ }
+ }
+ }
+
+ StockholmFile file = new StockholmFile(newAl);
+ String output = file.print(seqs, false);
+ PrintWriter writer = new PrintWriter(toFile);
+ writer.println(output);
+ writer.close();
+ }
+
+ /**
+ * Answers the full path to the given hmmer executable, or null if file cannot
+ * be found or is not executable
+ *
+ * @param cmd
+ * command short name e.g. hmmalign
+ * @return
+ */
+ protected String getCommandPath(String cmd)
+ {
+ String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+ File file = getExecutable(cmd, binariesFolder);
+ if (file == null && af != null)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmm_command_failed"));
+ }
+
+ return file == null ? null : file.getAbsolutePath();
+ }
+
+ /**
+ * Answers the executable file for the given hmmer command, or null if not
+ * found or not executable. The path to the executable is the command name
+ * prefixed by the hmmer binaries folder path, optionally with .exe appended.
+ *
+ * @param cmd
+ * hmmer command short name, for example hmmbuild
+ * @param binaryPath
+ * parent folder containing hmmer executables
+ * @return
+ */
+ public static File getExecutable(String cmd, String binaryPath)
+ {
+ File file = new File(binaryPath, cmd);
+ if (!file.canExecute())
+ {
+ file = new File(binaryPath, cmd + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ file = null;
+ }
+ }
+ }
+ return file;
+ }
+
+ /**
+ * A convenience method to create a temporary file that is deleted on exit of
+ * the JVM
+ *
+ * @param prefix
+ * @param suffix
+ * @return
+ * @throws IOException
+ */
+ protected File createTempFile(String prefix, String suffix)
+ throws IOException
+ {
+ File f = File.createTempFile(prefix, suffix);
+ f.deleteOnExit();
+ return f;
+
+ }
+
+ /**
+ * Exports an HMM to the specified file
+ *
+ * @param hmm
+ * @param hmmFile
+ * @throws IOException
+ */
+ public void exportHmm(HiddenMarkovModel hmm, File hmmFile)
+ throws IOException
+ {
+ if (hmm != null)
+ {
+ HMMFile file = new HMMFile(hmm);
+ PrintWriter writer = new PrintWriter(hmmFile);
+ writer.print(file.print());
+ writer.close();
+ }
+ }
+}
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
{
seqs.add(seq);
}
+
+ /**
+ * Used only for hmmer statistics, so should probably be removed at some
+ * point. TODO remove this
+ *
+ * @return
+ */
+ public Vector<AlignmentAnnotation> getAnnotations()
+ {
+ return annotations;
+ }
+
}
else
{
// consider deferring this till after the file has been parsed ?
- hidden.hideInsertionsFor(sr);
+ hidden.hideList(sr.getInsertions());
}
}
modified = true;
{
return false;
}
+ },
+ HMMER3("HMMER3", "hmm", true, true)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new HMMFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return new HMMFile();
+ }
};
+
private boolean writable;
private boolean readable;
return alignFrame;
}
+ public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+ String file, DataSourceType sourceType, FileFormatI format)
+ {
+ this.viewport = viewport;
+ this.file = file;
+ this.protocol = sourceType;
+ this.format = format;
+ _LoadAlignmentFileWaitTillLoaded();
+ }
+
+ protected void _LoadAlignmentFileWaitTillLoaded()
+ {
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
public void updateRecentlyOpened()
{
Vector recent = new Vector();
}
// append to existing alignment
viewport.addAlignment(al, title);
+ if (source instanceof HMMFile)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+ if (seq.isHMMConsensusSequence())
+ {
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ alignment.setHmmConsensus(seq);
+ }
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ }
}
else
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- hidden.makeVisibleAnnotation(selgp.getStartRes(),
- selgp.getEndRes(), na);
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
}
else
{
- hidden.makeVisibleAnnotation(na);
+ na.makeVisibleAnnotation(hidden);
}
alv.addAnnotation(na);
}
--- /dev/null
+package jalview.io;
+
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+
+/**
+ * Adds capability to read in and write out HMMER3 files. .
+ *
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMFile extends AlignFile
+ implements AlignmentFileReaderI, AlignmentFileWriterI
+{
+ private static final String TERMINATOR = "//";
+
+ /*
+ * keys to data in HMM file, used to store as properties of the HiddenMarkovModel
+ */
+ public static final String HMM = "HMM";
+
+ public static final String NAME = "NAME";
+
+ public static final String ACCESSION_NUMBER = "ACC";
+
+ public static final String DESCRIPTION = "DESC";
+
+ public static final String LENGTH = "LENG";
+
+ public static final String MAX_LENGTH = "MAXL";
+
+ public static final String ALPHABET = "ALPH";
+
+ public static final String DATE = "DATE";
+
+ public static final String COMMAND_LOG = "COM";
+
+ public static final String NUMBER_OF_SEQUENCES = "NSEQ";
+
+ public static final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+
+ public static final String CHECK_SUM = "CKSUM";
+
+ public static final String STATISTICS = "STATS";
+
+ public static final String COMPO = "COMPO";
+
+ public static final String GATHERING_THRESHOLD = "GA";
+
+ public static final String TRUSTED_CUTOFF = "TC";
+
+ public static final String NOISE_CUTOFF = "NC";
+
+ public static final String VITERBI = "VITERBI";
+
+ public static final String MSV = "MSV";
+
+ public static final String FORWARD = "FORWARD";
+
+ public static final String MAP = "MAP";
+
+ public static final String REFERENCE_ANNOTATION = "RF";
+
+ public static final String CONSENSUS_RESIDUE = "CONS";
+
+ public static final String CONSENSUS_STRUCTURE = "CS";
+
+ public static final String MASKED_VALUE = "MM";
+
+ private static final String ALPH_AMINO = "amino";
+
+ private static final String ALPH_DNA = "DNA";
+
+ private static final String ALPH_RNA = "RNA";
+
+ private static final String ALPHABET_AMINO = "ACDEFGHIKLMNPQRSTVWY";
+
+ private static final String ALPHABET_DNA = "ACGT";
+
+ private static final String ALPHABET_RNA = "ACGU";
+
+ private static final int NUMBER_OF_TRANSITIONS = 7;
+
+ private static final String SPACE = " ";
+
+ /*
+ * optional guide line added to an output HMMER file, purely for readability
+ */
+ private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
+
+ private static String NL = System.lineSeparator();
+
+ private HiddenMarkovModel hmm;
+
+ // number of symbols in the alphabet used in the hidden Markov model
+ private int numberOfSymbols;
+
+ /**
+ * Constructor that parses immediately
+ *
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public HMMFile(String inFile, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * Constructor that parses immediately
+ *
+ * @param source
+ * @throws IOException
+ */
+ public HMMFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Default constructor
+ */
+ public HMMFile()
+ {
+ }
+
+ /**
+ * Constructor for HMMFile used for exporting
+ *
+ * @param hmm
+ * @param exportImmediately
+ */
+ public HMMFile(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+
+ /**
+ * Returns the HMM produced by parsing a HMMER3 file
+ *
+ * @return
+ */
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ /**
+ * Gets the name of the hidden Markov model
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return hmm.getName();
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM model
+ */
+ @Override
+ public void parse()
+ {
+ try
+ {
+ hmm = new HiddenMarkovModel();
+ parseHeaderLines(dataIn);
+ parseModel(dataIn);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Reads the header properties from a HMMER3 file and saves them in the
+ * HiddeMarkovModel. This method exits after reading the next line after the
+ * HMM line.
+ *
+ * @param input
+ * @throws IOException
+ */
+ void parseHeaderLines(BufferedReader input) throws IOException
+ {
+ boolean readingHeaders = true;
+ hmm.setFileHeader(input.readLine());
+ String line = input.readLine();
+ while (readingHeaders && line != null)
+ {
+ Scanner parser = new Scanner(line);
+ String next = parser.next();
+ if (ALPHABET.equals(next))
+ {
+ String alphabetType = parser.next();
+ hmm.setProperty(ALPHABET, alphabetType);
+ String alphabet = ALPH_DNA.equalsIgnoreCase(alphabetType)
+ ? ALPHABET_DNA
+ : (ALPH_RNA.equalsIgnoreCase(alphabetType) ? ALPHABET_RNA
+ : ALPHABET_AMINO);
+ numberOfSymbols = hmm.setAlphabet(alphabet);
+ }
+ else if (HMM.equals(next))
+ {
+ readingHeaders = false;
+ String symbols = line.substring(line.indexOf(HMM) + HMM.length());
+ numberOfSymbols = hmm.setAlphabet(symbols);
+ }
+ else if (STATISTICS.equals(next))
+ {
+ parser.next();
+ String key;
+ String value;
+ key = parser.next();
+ value = parser.next() + SPACE + SPACE + parser.next();
+ hmm.setProperty(key, value);
+ }
+ else
+ {
+ String key = next;
+ String value = parser.next();
+ while (parser.hasNext())
+ {
+ value = value + SPACE + parser.next();
+ }
+ hmm.setProperty(key, value);
+ }
+ parser.close();
+ line = input.readLine();
+ }
+ }
+
+ /**
+ * Parses the model data from the HMMER3 file. The input buffer should be
+ * positioned at the (optional) COMPO line if there is one, else at the insert
+ * emissions line for the BEGIN node of the model.
+ *
+ * @param input
+ * @throws IOException
+ */
+ void parseModel(BufferedReader input) throws IOException
+ {
+ /*
+ * specification says there must always be an HMM header (already read)
+ * and one more header (guide headings) which is skipped here
+ */
+ int nodeNo = 0;
+ String line = input.readLine();
+ List<HMMNode> nodes = new ArrayList<>();
+
+ while (line != null && !TERMINATOR.equals(line))
+ {
+ HMMNode node = new HMMNode();
+ nodes.add(node);
+ Scanner scanner = new Scanner(line);
+ String next = scanner.next();
+
+ /*
+ * expect COMPO (optional) for average match emissions
+ * or a node number followed by node's match emissions
+ */
+ if (COMPO.equals(next) || nodeNo > 0)
+ {
+ /*
+ * parse match emissions
+ */
+ double[] matches = parseDoubles(scanner, numberOfSymbols);
+ node.setMatchEmissions(matches);
+ if (!COMPO.equals(next))
+ {
+ int resNo = parseAnnotations(scanner, node);
+ if (resNo == 0)
+ {
+ /*
+ * no MAP annotation provided, just number off from 0 (begin node)
+ */
+ resNo = nodeNo;
+ }
+ node.setResidueNumber(resNo);
+ }
+ line = input.readLine();
+ }
+ scanner.close();
+
+ /*
+ * parse insert emissions
+ */
+ scanner = new Scanner(line);
+ double[] inserts = parseDoubles(scanner, numberOfSymbols);
+ node.setInsertEmissions(inserts);
+ scanner.close();
+
+ /*
+ * parse state transitions
+ */
+ line = input.readLine();
+ scanner = new Scanner(line);
+ double[] transitions = parseDoubles(scanner,
+ NUMBER_OF_TRANSITIONS);
+ node.setStateTransitions(transitions);
+ scanner.close();
+ line = input.readLine();
+
+ nodeNo++;
+ }
+
+ hmm.setNodes(nodes);
+ }
+
+ /**
+ * Parses the annotations on the match emission line and add them to the node.
+ * (See p109 of the HMMER User Guide (V3.1b2) for the specification.) Returns
+ * the residue position that the node maps to, if provided, else zero.
+ *
+ * @param scanner
+ * @param node
+ */
+ int parseAnnotations(Scanner scanner, HMMNode node)
+ {
+ int mapTo = 0;
+
+ /*
+ * map from hmm node to sequence position, if provided
+ */
+ if (scanner.hasNext())
+ {
+ String value = scanner.next();
+ if (!"-".equals(value))
+ {
+ try
+ {
+ mapTo = Integer.parseInt(value);
+ node.setResidueNumber(mapTo);
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+ }
+
+ /*
+ * hmm consensus residue if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setConsensusResidue(scanner.next().charAt(0));
+ }
+
+ /*
+ * RF reference annotation, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setReferenceAnnotation(scanner.next().charAt(0));
+ }
+
+ /*
+ * 'm' for masked position, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setMaskValue(scanner.next().charAt(0));
+ }
+
+ /*
+ * structure consensus symbol, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setConsensusStructure(scanner.next().charAt(0));
+ }
+
+ return mapTo;
+ }
+
+ /**
+ * Fills an array of doubles parsed from an input line
+ *
+ * @param input
+ * @param numberOfElements
+ * @return
+ * @throws IOException
+ */
+ static double[] parseDoubles(Scanner input,
+ int numberOfElements) throws IOException
+ {
+ double[] values = new double[numberOfElements];
+ for (int i = 0; i < numberOfElements; i++)
+ {
+ if (!input.hasNext())
+ {
+ throw new IOException("Incomplete data");
+ }
+ String next = input.next();
+ if (next.contains("*"))
+ {
+ values[i] = Double.NEGATIVE_INFINITY;
+ }
+ else
+ {
+ double prob = Double.valueOf(next);
+ prob = Math.pow(Math.E, -prob);
+ values[i] = prob;
+ }
+ }
+ return values;
+ }
+
+ /**
+ * Returns a string to be added to the StringBuilder containing the entire
+ * output String.
+ *
+ * @param initialColumnSeparation
+ * The initial whitespace separation between the left side of the
+ * file and first character.
+ * @param columnSeparation
+ * The separation between subsequent data entries.
+ * @param data
+ * The list of data to be added to the String.
+ * @return
+ */
+ String addData(int initialColumnSeparation,
+ int columnSeparation, List<String> data)
+ {
+ String line = "";
+ boolean first = true;
+ for (String value : data)
+ {
+ int sep = first ? initialColumnSeparation : columnSeparation;
+ line += String.format("%" + sep + "s", value);
+ first = false;
+ }
+ return line;
+ }
+
+ /**
+ * Converts list of characters into a list of Strings.
+ *
+ * @param list
+ * @return Returns the list of Strings.
+ */
+ List<String> charListToStringList(List<Character> list)
+ {
+ List<String> strList = new ArrayList<>();
+ for (char value : list)
+ {
+ String strValue = Character.toString(value);
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Converts an array of doubles into a list of Strings, rounded to the nearest
+ * 5th decimal place
+ *
+ * @param doubles
+ * @param noOfDecimals
+ * @return
+ */
+ List<String> doublesToStringList(double[] doubles)
+ {
+ List<String> strList = new ArrayList<>();
+ for (double value : doubles)
+ {
+ String strValue;
+ if (value > 0)
+ {
+ strValue = String.format("%.5f", value);
+ }
+ else if (value == -0.00000d)
+ {
+ strValue = "0.00000";
+ }
+ else
+ {
+ strValue = "*";
+ }
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Appends model data in string format to the string builder
+ *
+ * @param output
+ */
+ void appendModelAsString(StringBuilder output)
+ {
+ output.append(HMM).append(" ");
+ String charSymbols = hmm.getSymbols();
+ for (char c : charSymbols.toCharArray())
+ {
+ output.append(String.format("%9s", c));
+ }
+ output.append(NL).append(TRANSITIONTYPELINE);
+
+ int length = hmm.getLength();
+
+ for (int nodeNo = 0; nodeNo <= length; nodeNo++)
+ {
+ String matchLine = String.format("%7s",
+ nodeNo == 0 ? COMPO : Integer.toString(nodeNo));
+
+ double[] doubleMatches = convertToLogSpace(
+ hmm.getNode(nodeNo).getMatchEmissions());
+ List<String> strMatches = doublesToStringList(doubleMatches);
+ matchLine += addData(10, 9, strMatches);
+
+ if (nodeNo != 0)
+ {
+ matchLine += SPACE + (hmm.getNodeMapPosition(nodeNo));
+ matchLine += SPACE + hmm.getConsensusResidue(nodeNo);
+ matchLine += SPACE + hmm.getReferenceAnnotation(nodeNo);
+ if (hmm.getFileHeader().contains("HMMER3/f"))
+ {
+ matchLine += SPACE + hmm.getMaskedValue(nodeNo);
+ matchLine += SPACE + hmm.getConsensusStructure(nodeNo);
+ }
+ }
+
+ output.append(NL).append(matchLine);
+
+ String insertLine = "";
+
+ double[] doubleInserts = convertToLogSpace(
+ hmm.getNode(nodeNo).getInsertEmissions());
+ List<String> strInserts = doublesToStringList(doubleInserts);
+ insertLine += addData(17, 9, strInserts);
+
+ output.append(NL).append(insertLine);
+
+ String transitionLine = "";
+ double[] doubleTransitions = convertToLogSpace(
+ hmm.getNode(nodeNo).getStateTransitions());
+ List<String> strTransitions = doublesToStringList(
+ doubleTransitions);
+ transitionLine += addData(17, 9, strTransitions);
+
+ output.append(NL).append(transitionLine);
+ }
+ }
+
+ /**
+ * Appends formatted HMM file properties to the string builder
+ *
+ * @param output
+ */
+ void appendProperties(StringBuilder output)
+ {
+ output.append(hmm.getFileHeader());
+
+ String format = "%n%-5s %1s";
+ appendProperty(output, format, NAME);
+ appendProperty(output, format, ACCESSION_NUMBER);
+ appendProperty(output, format, DESCRIPTION);
+ appendProperty(output, format, LENGTH);
+ appendProperty(output, format, MAX_LENGTH);
+ appendProperty(output, format, ALPHABET);
+ appendBooleanProperty(output, format, REFERENCE_ANNOTATION);
+ appendBooleanProperty(output, format, MASKED_VALUE);
+ appendBooleanProperty(output, format, CONSENSUS_RESIDUE);
+ appendBooleanProperty(output, format, CONSENSUS_STRUCTURE);
+ appendBooleanProperty(output, format, MAP);
+ appendProperty(output, format, DATE);
+ appendProperty(output, format, NUMBER_OF_SEQUENCES);
+ appendProperty(output, format, EFF_NUMBER_OF_SEQUENCES);
+ appendProperty(output, format, CHECK_SUM);
+ appendProperty(output, format, GATHERING_THRESHOLD);
+ appendProperty(output, format, TRUSTED_CUTOFF);
+ appendProperty(output, format, NOISE_CUTOFF);
+
+ if (hmm.getMSV() != null)
+ {
+ format = "%n%-19s %18s";
+ output.append(String.format(format, "STATS LOCAL MSV", hmm.getMSV()));
+
+ output.append(String.format(format, "STATS LOCAL VITERBI",
+ hmm.getViterbi()));
+
+ output.append(String.format(format, "STATS LOCAL FORWARD",
+ hmm.getForward()));
+ }
+ }
+
+ /**
+ * Appends 'yes' or 'no' for the given property, according to whether or not
+ * it is set in the HMM
+ *
+ * @param output
+ * @param format
+ * @param propertyName
+ */
+ private void appendBooleanProperty(StringBuilder output, String format,
+ String propertyName)
+ {
+ boolean set = hmm.getBooleanProperty(propertyName);
+ output.append(String.format(format, propertyName,
+ set ? HiddenMarkovModel.YES : HiddenMarkovModel.NO));
+ }
+
+ /**
+ * Appends the value of the given property to the output, if not null
+ *
+ * @param output
+ * @param format
+ * @param propertyName
+ */
+ private void appendProperty(StringBuilder output, String format,
+ String propertyName)
+ {
+ String value = hmm.getProperty(propertyName);
+ if (value != null)
+ {
+ output.append(String.format(format, propertyName, value));
+ }
+ }
+
+ @Override
+ public String print(SequenceI[] sequences, boolean jvsuffix)
+ {
+ if (sequences[0].getHMM() != null)
+ {
+ hmm = sequences[0].getHMM();
+ }
+ return print();
+ }
+
+ /**
+ * Prints the .hmm file to a String.
+ *
+ * @return
+ */
+ public String print()
+ {
+ StringBuilder output = new StringBuilder();
+ appendProperties(output);
+ output.append(NL);
+ appendModelAsString(output);
+ output.append(NL).append(TERMINATOR).append(NL);
+ return output.toString();
+ }
+
+ /**
+ * Converts the probabilities contained in an array into log space
+ *
+ * @param ds
+ */
+ double[] convertToLogSpace(double[] ds)
+ {
+ double[] converted = new double[ds.length];
+ for (int i = 0; i < ds.length; i++)
+ {
+ double prob = ds[i];
+ double logProb = -1 * Math.log(prob);
+
+ converted[i] = logProb;
+ }
+ return converted;
+ }
+
+ /**
+ * Returns the HMM sequence produced by reading a .hmm file.
+ */
+ @Override
+ public SequenceI[] getSeqsAsArray()
+ {
+ SequenceI hmmSeq = hmm.getConsensusSequence();
+ SequenceI[] seq = new SequenceI[1];
+ seq[0] = hmmSeq;
+ return seq;
+ }
+
+ @Override
+ public void setNewlineString(String newLine)
+ {
+ NL = newLine;
+ }
+
+ @Override
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+
+ }
+
+ @Override
+ public void configureForView(AlignmentViewPanel viewpanel)
+ {
+
+ }
+
+ @Override
+ public boolean hasWarningMessage()
+ {
+ return false;
+ }
+
+ @Override
+ public String getWarningMessage()
+ {
+ return "warning message";
+ }
+
+}
+
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("HMMER3"))
+ {
+ reply = FileFormat.HMMER3;
+ break;
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
import com.stevesoft.pat.Regex;
{
private static final String ANNOTATION = "annotation";
- private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ private static final char UNDERSCORE = '_';
- private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+ // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
public static final Regex DETECT_BRACKETS = new Regex(
"(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
- StringBuffer out; // output buffer
+ /*
+ * lookup table of Stockholm 'feature' (annotation) types
+ * see http://sonnhammer.sbc.su.se/Stockholm.html
+ */
+ private static Map<String, String> featureTypes = null;
+
+ static
+ {
+ featureTypes = new HashMap<>();
+ featureTypes.put("SS", "Secondary Structure");
+ featureTypes.put("SA", "Surface Accessibility");
+ featureTypes.put("TM", "transmembrane");
+ featureTypes.put("PP", "Posterior Probability");
+ featureTypes.put("LI", "ligand binding");
+ featureTypes.put("AS", "active site");
+ featureTypes.put("IN", "intron");
+ featureTypes.put("IR", "interacting residue");
+ featureTypes.put("AC", "accession");
+ featureTypes.put("OS", "organism");
+ featureTypes.put("CL", "class");
+ featureTypes.put("DE", "description");
+ featureTypes.put("DR", "reference");
+ featureTypes.put("LO", "look");
+ featureTypes.put("RF", "Reference Positions");
+ }
- AlignmentI al;
+ private AlignmentI al;
public StockholmFile()
{
}
/**
- * Creates a new StockholmFile object for output.
+ * Creates a new StockholmFile object for output
*/
public StockholmFile(AlignmentI al)
{
super(source);
}
+ /**
+ * Answers the readable description for a (case-sensitive) annotation type
+ * code, for example "Reference Positions" for "RF". Returns the type code if
+ * no description is found.
+ *
+ * @param id
+ * @return
+ */
+ public static String typeToDescription(String id)
+ {
+ if (featureTypes.containsKey(id))
+ {
+ return featureTypes.get(id);
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type code " + id);
+ return id;
+ }
+
+ /**
+ * Answers the annotation type code for a (non-case-sensitive) readable
+ * description, for example "RF" for "Reference Positions" (or null if not
+ * found)
+ *
+ * @param description
+ * @return
+ */
+ public static String descriptionToType(String description)
+ {
+ for (Entry<String, String> entry : featureTypes.entrySet())
+ {
+ if (entry.getValue().equalsIgnoreCase(description))
+ {
+ return entry.getKey();
+ }
+ }
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type: " + description);
+ return null;
+ }
+
@Override
public void initData()
{
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
// logger.debug("Stockholm version: " + version);
}
- // We define some Regexes here that will be used regularily later
+ // We define some Regexes here that will be used regularly later
rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
// id/from/to
Regex closeparen = new Regex("(>|\\])", ")");
// Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
Hashtable content = (Hashtable) features.remove(type);
// add alignment annotation for this feature
- String key = type2id(type);
+ String key = descriptionToType(type);
/*
* have we added annotation rows for this type ?
}
Hashtable content;
- if (features.containsKey(this.id2type(type)))
+ if (features.containsKey(StockholmFile.typeToDescription(type)))
{
// logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
+ content = (Hashtable) features
+ .get(StockholmFile.typeToDescription(type));
}
else
{
// logger.debug("Creating new content holder for " +
// this.id2type(type));
content = new Hashtable();
- features.put(this.id2type(type), content);
+ features.put(StockholmFile.typeToDescription(type), content);
}
String ns = (String) content.get(ANNOTATION);
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
Vector<AlignmentAnnotation> annotation, String label,
String annots)
{
- String convert1, convert2 = null;
-
- // convert1 = OPEN_PAREN.replaceAll(annots);
- // convert2 = CLOSE_PAREN.replaceAll(convert1);
+ // String convert1 = OPEN_PAREN.replaceAll(annots);
+ // String convert2 = CLOSE_PAREN.replaceAll(convert1);
// annots = convert2;
String type = label;
: label;
}
boolean ss = false, posterior = false;
- type = id2type(type);
+ type = typeToDescription(type);
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);
+ if (UNDERSCORE == pos.charAt(0))
+ {
+ pos = " ";
+ }
Annotation ann;
ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
// be written out
}
@Override
- public String print(SequenceI[] s, boolean jvSuffix)
+ public String print(final SequenceI[] sequences, boolean jvSuffix)
{
- out = new StringBuffer();
+ StringBuilder out = new StringBuilder();
out.append("# STOCKHOLM 1.0");
out.append(newline);
- // find max length of id
- int max = 0;
- int maxid = 0;
- int in = 0;
- Hashtable dataRef = null;
- while ((in < s.length) && (s[in] != null))
+ int maxIdWidth = 0;
+ for (SequenceI seq : sequences)
{
- String tmp = printId(s[in], jvSuffix);
- max = Math.max(max, s[in].getLength());
-
- if (tmp.length() > maxid)
- {
- maxid = tmp.length();
- }
- if (s[in].getDBRefs() != null)
+ if (seq != null)
{
- for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
- {
- if (dataRef == null)
- {
- dataRef = new Hashtable();
- }
-
- String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
- + " ; "
- + s[in].getDBRefs()[idb].getAccessionId().toString();
- dataRef.put(tmp, datAs1);
- }
+ String formattedId = printId(seq, jvSuffix);
+ maxIdWidth = Math.max(maxIdWidth, formattedId.length());
}
- in++;
}
- maxid += 9;
- int i = 0;
+ maxIdWidth += 9;
- // output database type
- if (al.getProperties() != null)
+ /*
+ * generic alignment properties
+ */
+ Hashtable props = al.getProperties();
+ if (props != null)
{
- if (!al.getProperties().isEmpty())
+ for (Object key : props.keySet())
{
- Enumeration key = al.getProperties().keys();
- Enumeration val = al.getProperties().elements();
- while (key.hasMoreElements())
- {
- out.append("#=GF " + key.nextElement() + " " + val.nextElement());
- out.append(newline);
- }
+ out.append(String.format("#=GF %s %s", key.toString(),
+ props.get(key).toString()));
+ out.append(newline);
}
}
- // output database accessions
- if (dataRef != null)
+ /*
+ * output database accessions as #=GS (per sequence annotation)
+ * PFAM or RFAM are output as AC <accession number>
+ * others are output as DR <dbname> ; <accession>
+ */
+ Format formatter = new Format("%-" + (maxIdWidth - 2) + "s");
+ for (SequenceI seq : sequences)
{
- Enumeration en = dataRef.keys();
- while (en.hasMoreElements())
+ if (seq != null)
{
- Object idd = en.nextElement();
- String type = (String) dataRef.remove(idd);
- out.append(new Format("%-" + (maxid - 2) + "s")
- .form("#=GS " + idd.toString() + " "));
- if (type.contains("PFAM") || type.contains("RFAM"))
- {
-
- out.append(" AC " + type.substring(type.indexOf(";") + 1));
- }
- else
+ DBRefEntry[] dbRefs = seq.getDBRefs();
+ if (dbRefs != null)
{
- out.append(" DR " + type + " ");
+ String idField = formatter
+ .form("#=GS " + printId(seq, jvSuffix) + " ");
+ for (DBRefEntry dbRef : dbRefs)
+ {
+ out.append(idField);
+ printDbRef(out, dbRef);
+ }
}
- out.append(newline);
}
}
- // output annotations
- while (i < s.length && s[i] != null)
+ /*
+ * output annotations
+ */
+ for (SequenceI seq : sequences)
{
- AlignmentAnnotation[] alAnot = s[i].getAnnotation();
- if (alAnot != null)
+ if (seq != null)
{
- Annotation[] ann;
- for (int j = 0; j < alAnot.length; j++)
+ AlignmentAnnotation[] alAnot = seq.getAnnotation();
+ if (alAnot != null)
{
-
- String key = type2id(alAnot[j].label);
- boolean isrna = alAnot[j].isValidStruc();
-
- if (isrna)
- {
- // hardwire to secondary structure if there is RNA secondary
- // structure on the annotation
- key = "SS";
- }
- if (key == null)
+ for (int j = 0; j < alAnot.length; j++)
{
+ AlignmentAnnotation ann = alAnot[j];
+ String key = descriptionToType(ann.label);
+ boolean isrna = ann.isValidStruc();
+ if (isrna)
+ {
+ /*
+ * output as secondary structure if there is
+ * RNA secondary structure on the annotation
+ */
+ key = "SS";
+ }
+ if (key == null)
+ {
+ continue;
+ }
- continue;
- }
-
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form(
- "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
- ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
- {
- seq += outputCharacter(key, k, isrna, ann, s[i]);
+ out.append(new Format("%-" + maxIdWidth + "s").form(
+ "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
+ Annotation[] anns = ann.annotations;
+ StringBuilder seqString = new StringBuilder();
+ for (int k = 0; k < anns.length; k++)
+ {
+ seqString
+ .append(getAnnotationCharacter(key, k, anns[k], seq));
+ }
+ out.append(seqString.toString());
+ out.append(newline);
}
- out.append(seq);
- out.append(newline);
}
- }
- out.append(new Format("%-" + maxid + "s")
- .form(printId(s[i], jvSuffix) + " "));
- out.append(s[i].getSequenceAsString());
- out.append(newline);
- i++;
+ out.append(new Format("%-" + maxIdWidth + "s")
+ .form(printId(seq, jvSuffix) + " "));
+ out.append(seq.getSequenceAsString());
+ out.append(newline);
+ }
}
- // alignment annotation
- AlignmentAnnotation aa;
+ /*
+ * output alignment annotation (but not auto-calculated or sequence-related)
+ */
if (al.getAlignmentAnnotation() != null)
{
for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
{
- aa = al.getAlignmentAnnotation()[ia];
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
{
continue;
}
- String seq = "";
- String label;
+ String label = aa.label;
String key = "";
if (aa.label.equals("seq"))
{
}
else
{
- key = type2id(aa.label.toLowerCase());
- if (key == null)
+ key = descriptionToType(aa.label);
+ if ("RF".equals(key))
{
- label = aa.label;
+ label = key;
}
- else
+ else if (key != null)
{
label = key + "_cons";
}
}
- if (label == null)
- {
- label = aa.label;
- }
label = label.replace(" ", "_");
out.append(
- new Format("%-" + maxid + "s").form("#=GC " + label + " "));
- boolean isrna = aa.isValidStruc();
+ new Format("%-" + maxIdWidth + "s")
+ .form("#=GC " + label + " "));
+ StringBuilder sb = new StringBuilder(aa.annotations.length);
for (int j = 0; j < aa.annotations.length; j++)
{
- seq += outputCharacter(key, j, isrna, aa.annotations, null);
+ sb.append(
+ getAnnotationCharacter(key, j, aa.annotations[j], null));
}
- out.append(seq);
+ out.append(sb.toString());
out.append(newline);
}
}
}
/**
- * add an annotation character to the output row
+ * A helper method that appends a formatted dbref to the output buffer
+ *
+ * @param out
+ * @param dbRef
+ */
+ protected void printDbRef(StringBuilder out, DBRefEntry dbRef)
+ {
+ String db = dbRef.getSource();
+ String acc = dbRef.getAccessionId();
+ if (DBRefSource.PFAM.equalsIgnoreCase(db)
+ || DBRefSource.RFAM.equalsIgnoreCase(db))
+ {
+ out.append(" AC " + acc);
+ }
+ else
+ {
+ out.append(" DR " + db + " ; " + acc);
+ }
+ out.append(newline);
+ }
+
+ /**
+ * Returns an annotation character to add to the output row
*
* @param seq
* @param key
* @param k
- * @param isrna
* @param ann
* @param sequenceI
*/
- private char outputCharacter(String key, int k, boolean isrna,
- Annotation[] ann, SequenceI sequenceI)
+ static char getAnnotationCharacter(String key, int k, Annotation annot,
+ SequenceI sequenceI)
{
char seq = ' ';
- Annotation annot = ann[k];
String ch = (annot == null)
? ((sequenceI == null) ? "-"
: Character.toString(sequenceI.getCharAt(k)))
{
if (annot == null)
{
- // sensible gap character
- return ' ';
+ // Stockholm format requires underscore, not space
+ return UNDERSCORE;
}
else
{
return seq;
}
- public String print()
- {
- out = new StringBuffer();
- out.append("# STOCKHOLM 1.0");
- out.append(newline);
- print(getSeqsAsArray(), false);
-
- out.append("//");
- out.append(newline);
- return out.toString();
- }
-
- private static Hashtable typeIds = null;
-
- static
- {
- if (typeIds == null)
- {
- typeIds = new Hashtable();
- typeIds.put("SS", "Secondary Structure");
- typeIds.put("SA", "Surface Accessibility");
- typeIds.put("TM", "transmembrane");
- typeIds.put("PP", "Posterior Probability");
- typeIds.put("LI", "ligand binding");
- typeIds.put("AS", "active site");
- typeIds.put("IN", "intron");
- typeIds.put("IR", "interacting residue");
- typeIds.put("AC", "accession");
- typeIds.put("OS", "organism");
- typeIds.put("CL", "class");
- typeIds.put("DE", "description");
- typeIds.put("DR", "reference");
- typeIds.put("LO", "look");
- typeIds.put("RF", "Reference Positions");
-
- }
- }
-
- protected static String id2type(String id)
- {
- if (typeIds.containsKey(id))
- {
- return (String) typeIds.get(id);
- }
- System.err.println(
- "Warning : Unknown Stockholm annotation type code " + id);
- return id;
- }
-
- protected static String type2id(String type)
- {
- String key = null;
- Enumeration e = typeIds.keys();
- while (e.hasMoreElements())
- {
- Object ll = e.nextElement();
- if (typeIds.get(ll).toString().equalsIgnoreCase(type))
- {
- key = (String) ll;
- break;
- }
- }
- if (key != null)
- {
- return key;
- }
- System.err.println(
- "Warning : Unknown Stockholm annotation type: " + type);
- return key;
- }
-
/**
* make a friendly ID string.
*
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
protected JMenu webService = new JMenu();
+ protected JMenu hmmerMenu = new JMenu();
+
+ protected JMenu hmmAlign = new JMenu();
+
+ protected JMenuItem hmmAlignRun = new JMenuItem();
+
+ protected JMenuItem hmmAlignSettings = new JMenuItem();
+
+ protected JMenu hmmSearch = new JMenu();
+
+ protected JMenuItem hmmSearchRun = new JMenuItem();
+
+ protected JMenuItem hmmSearchSettings = new JMenuItem();
+
+ protected JMenuItem addDatabase = new JMenuItem();
+
+ protected JMenu hmmBuild = new JMenu();
+
+ protected JMenuItem hmmBuildRun = new JMenuItem();
+
+ protected JMenuItem hmmBuildSettings = new JMenuItem();
+
protected JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
private void jbInit() throws Exception
{
initColourMenu();
-
+ initHMMERMenu();
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed(e);
}
};
-
+
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
JMenu annotationsMenu = new JMenu(
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ hmmerMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmerMenu_actionPerformed(e);
+ }
+ });
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
}
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+
JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.deselect_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
}
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+
JMenuItem grpsFromSelection = new JMenuItem(
MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new ActionListener()
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
}
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+
JMenuItem justifyLeftMenuItem = new JMenuItem(
MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem.addActionListener(new ActionListener()
sortGroupMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
}
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
-
+
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
-
+
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
+
outputTextboxMenu
.setText(MessageManager.getString("label.out_to_textbox"));
+
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
+
sortAnnBySequence.setSelected(
sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
colourTextMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem htmlMenuItem = new JMenuItem(
MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new ActionListener()
htmlMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem createBioJS = new JMenuItem(
MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
bioJSMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem overviewMenuItem = new JMenuItem(
MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new ActionListener()
overviewMenuItem_actionPerformed(e);
}
});
-
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
}
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
wrapMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
}
};
addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
showSeqFeatures.setText(
MessageManager.getString("label.show_sequence_features"));
+
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
.setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
showNpFeatsMenuitem.setText(
MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
showGroupConservation
.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
showGroupConsensus
.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
showConsensusHistogram.setText(
MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
});
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
-
+
});
normaliseSequenceLogo
.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
applyAutoAnnotationSettings
.setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings_actionPerformed(e);
}
});
-
+
ButtonGroup buttonGroup = new ButtonGroup();
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
MessageManager.getString("label.show_first"));
sortAnnotations_actionPerformed();
}
});
-
+
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
}
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+
JMenuItem annotationColumn = new JMenuItem(
MessageManager.getString("action.select_by_annotation"));
annotationColumn.addActionListener(new ActionListener()
annotationColumn_actionPerformed(e);
}
});
-
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
-
+
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
-
+
JMenuItem delete = new JMenuItem(
MessageManager.getString("action.delete"));
delete.addActionListener(new ActionListener()
delete_actionPerformed(e);
}
});
-
+
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
@Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ try
+ {
+ pasteNew_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
@Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ try
+ {
+ pasteThis_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
});
createPNG.setActionCommand(
MessageManager.getString("label.save_png_image"));
-
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
createEPS(null);
}
});
-
+
JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
{
createSVG(null);
}
});
-
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
loadTreeMenuItem.setActionCommand(
loadTreeMenuItem_actionPerformed(e);
}
});
-
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new ActionListener()
.setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
}
-
+
});
-
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
{
buildTreeSortMenu();
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuCanceled(MenuEvent e)
{
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
-
+
@Override
public void menuCanceled(MenuEvent e)
{
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuSelected(MenuEvent e)
{
showReverse_actionPerformed(true);
}
});
-
+
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
extractScores.addActionListener(new ActionListener()
});
extractScores.setVisible(true);
// JBPNote: TODO: make gui for regex based score extraction
-
+
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+
runGroovy.setText(MessageManager.getString("label.run_groovy"));
runGroovy.setToolTipText(
MessageManager.getString("label.run_groovy_tip"));
runGroovy_actionPerformed();
}
});
-
+
JMenuItem openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
fetchSequence_actionPerformed(e);
}
});
-
+
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ try
+ {
+ associatedData_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
listenToViewSelections_actionPerformed(e);
}
});
-
+
JMenu addSequenceMenu = new JMenu(
MessageManager.getString("label.add_sequences"));
JMenuItem addFromFile = new JMenuItem(
hiddenMarkers_actionPerformed(e);
}
});
-
+
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
}
};
addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+
showComplementMenuItem.setVisible(false);
showComplementMenuItem.addActionListener(new ActionListener()
{
showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
-
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_mousePressed(e);
}
}
-
+
@Override
public void mouseReleased(MouseEvent e)
{
tabbedPane_focusGained(e);
}
});
-
+
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, save, al);
-
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
-
+
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
}
};
addMenuActionAndAccelerator(keyStroke, newView, al);
-
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
-
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign_actionPerformed(e);
}
});
-
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+
JMenuItem pageSetup = new JMenuItem(
MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
+ hmmBuildRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(true);
+ }
+ });
+ hmmBuildSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(false);
+ }
+ });
+ hmmAlignRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlignRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(true);
+ }
+ });
+ hmmAlignSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(false);
+ }
+ });
+ hmmSearchRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(true);
+ }
+ });
+ hmmSearchSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(false);
+ }
+ });
+ addDatabase.setText(MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
-
+ alignFrameMenuBar.add(hmmerMenu);
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
fileMenu.add(loadVcf);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
-
+
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
-
+
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
showMenu.add(showAllhidden);
viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
-
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAllAlAnnotations);
calculateMenu.add(extractScores);
calculateMenu.addSeparator();
calculateMenu.add(runGroovy);
-
+
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
// selectMenu.add(listenToViewSelections);
}
+ public void hmmerMenu_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ /**
+ * Constructs the entries on the HMMER menu (does not add them to the menu).
+ */
+ protected void initHMMERMenu()
+ {
+ hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+ hmmAlignSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlign.add(hmmAlignSettings);
+ hmmAlign.add(hmmAlignRun);
+ hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ hmmBuildSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuild.add(hmmBuildSettings);
+ hmmBuild.add(hmmBuildRun);
+ hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
+ hmmSearchSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ hmmSearch.add(hmmSearchSettings);
+ hmmSearch.add(hmmSearchRun);
+ hmmSearch.add(addDatabase);
+ }
+
protected void loadVcf_actionPerformed()
{
}
}
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
{
}
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
+ {
+ }
+
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ }
+
public void createPNG(java.io.File f)
{
}
}
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import javax.swing.AbstractButton;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
+
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
+
/*
* Structure tab and components
*/
protected JCheckBox sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab = new JPanel();
+
+ protected JCheckBox hmmrTrimTermini = new JCheckBox();
+
+ protected AbstractButton hmmerBackgroundUniprot = new JCheckBox();
+
+ protected AbstractButton hmmerBackgroundAlignment = new JCheckBox();
+
+ protected JTextField hmmerSequenceCount = new JTextField();
+
+ protected JTextField hmmerPath = new JTextField();
+
+ /*
* DAS Settings tab
*/
protected JPanel dasTab = new JPanel();
*/
protected JPanel wsTab = new JPanel();
+
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
/*
* See DasSourceBrowser for the real work of configuring this tab.
*/
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
/**
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab.setLayout(null);
+
+ JLabel installationLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ installationLocation.setFont(LABEL_FONT);
+ installationLocation.setBounds(new Rectangle(22, 10, 250, 23));
+ hmmerPath.setBounds(new Rectangle(22, 30, 300, 23));
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ }
+ }
+ }
+ });
+
+ JLabel hmmalign = new JLabel(
+ MessageManager.getString("label.hmmalign_label"));
+ hmmalign.setFont(LABEL_FONT);
+ hmmalign.setBounds(new Rectangle(22, 50, 200, 23));
+
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ hmmrTrimTermini.setBounds(new Rectangle(22, 70, 200, 23));
+
+ JLabel hmmsearch = new JLabel(
+ MessageManager.getString("label.hmmsearch_label"));
+ hmmsearch.setFont(LABEL_FONT);
+ hmmsearch.setBounds(new Rectangle(22, 90, 200, 23));
+
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ sequencesToKeep.setBounds(new Rectangle(22, 110, 125, 23));
+ hmmerSequenceCount.setBounds(new Rectangle(150, 110, 40, 23));
+
+ ButtonGroup backgroundFreqSource = new ButtonGroup();
+ backgroundFreqSource.add(hmmerBackgroundUniprot);
+ backgroundFreqSource.add(hmmerBackgroundAlignment);
+ backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true);
+
+ hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundUniprot.setBounds(new Rectangle(22, 130, 255, 23));
+
+ hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment.setBounds(new Rectangle(22, 150, 300, 23));
+
+ hmmerTab.add(hmmerBackgroundUniprot);
+ hmmerTab.add(hmmerBackgroundAlignment);
+ hmmerTab.add(hmmalign);
+ hmmerTab.add(hmmsearch);
+ hmmerTab.add(installationLocation);
+ hmmerTab.add(hmmerPath);
+ hmmerTab.add(hmmrTrimTermini);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(hmmerSequenceCount);
+
+ return hmmerTab;
+ }
+
+ /**
* Initialises the Output tabbed panel.
*
* @return
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
*
* @return
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
return choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
+ protected boolean validateStructure()
{
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
+ return false;
}
- protected boolean validateStructure()
+ protected boolean validateHMMERPath(boolean showWarning)
{
return false;
}
}
}
+
+ public void hmmerPath_actionPerformed(ActionEvent e)
+ {
+
+ }
}
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
+import jalview.workers.InformationThread;
import java.awt.BasicStroke;
import java.awt.Color;
private final boolean MAC = Platform.isAMac();
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
+ // todo remove these flags, read from group/viewport where needed
+ boolean av_renderHistogram = true;
+
+ boolean av_renderProfile = true;
+
+ boolean av_normaliseProfile = false;
+
+ boolean av_infoHeight = false;
ResidueShaderI profcolour = null;
private boolean av_ignoreGapsConsensus;
+ private boolean av_ignoreBelowBackground;
+
/**
* attributes set from AwtRenderPanelI
*/
{
g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth)
- + hiddenColumns.adjustForHiddenColumns(startRes);
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth)
- + hiddenColumns.adjustForHiddenColumns(startRes);
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
}
columnSelection = av.getColumnSelection();
hiddenColumns = av.getAlignment().getHiddenColumns();
- hconsensus = av.getSequenceConsensusHash();
+ hconsensus = av.getConsensusProfiles();
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+ av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+ av_infoHeight = av.isInfoLetterHeight();
}
+
+
/**
* Returns profile data; the first element is the profile type, the second is
* the number of distinct values, the third the total count, and the remainder
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && (aa.label.startsWith("Consensus")
- || aa.label.startsWith("cDNA Consensus")))
+ if (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
+ {
+ HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+ return AAFrequency.extractHMMProfile(hmm, column,
+ av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
+ // pipeline
+ }
+ if (aa.autoCalculated
+ && (aa.label.startsWith("Consensus") || aa.label
+ .startsWith("cDNA Consensus")))
{
boolean forComplement = aa.label.startsWith("cDNA Consensus");
- if (aa.groupRef != null && aa.groupRef.consensusData != null
+ if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
&& aa.groupRef.isShowSequenceLogo())
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData.get(column),
- aa.groupRef.getIgnoreGapsConsensus());
+ aa.groupRef.getConsensusData().get(column),
+ aa.groupRef.isIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
}
+ else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
+ {
+ if (row.groupRef != null)
+ {
+ renderHistogram = row.groupRef.isShowInformationHistogram();
+ renderProfile = row.groupRef.isShowHMMSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
+ }
+ else
+ {
+ renderHistogram = av.isShowInformationHistogram();
+ renderProfile = av.isShowHMMSequenceLogo();
+ normaliseProfile = av.isNormaliseHMMSequenceLogo();
+ }
+ }
else
{
renderHistogram = true;
{
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(startRes + x);
+ column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
if (column > row_annotations.length - 1)
{
break;
g.setColor(HELIX_COLOUR);
int sCol = (lastSSX / charWidth)
- + hiddenColumns.adjustForHiddenColumns(startRes);
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
column = sRes + x;
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)
column = sRes + x;
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
+ * PURPOSE. See the GNU General License for more details.
*
- * You should have received a copy of the GNU General Public License
+ * You should have received a copy of the GNU General License
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
public interface ResidueShaderI
{
+ void setConsensus(ProfilesI cons);
- public abstract void setConsensus(ProfilesI cons);
+ boolean conservationApplied();
- public abstract boolean conservationApplied();
+ void setConservationApplied(boolean conservationApplied);
- public abstract void setConservationApplied(boolean conservationApplied);
+ void setConservation(Conservation cons);
- public abstract void setConservation(Conservation cons);
-
- public abstract void alignmentChanged(AnnotatedCollectionI alignment,
+ void alignmentChanged(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps);
/**
* @param consensusThreshold
* @param ignoreGaps
*/
- public abstract void setThreshold(int consensusThreshold,
+ void setThreshold(int consensusThreshold,
boolean ignoreGaps);
- public abstract void setConservationInc(int i);
+ void setConservationInc(int i);
- public abstract int getConservationInc();
+ int getConservationInc();
/**
* Get the percentage threshold for this colour scheme
*
* @return Returns the percentage threshold
*/
- public abstract int getThreshold();
+ int getThreshold();
/**
* Returns the possibly context dependent colour for the given symbol at the
* @param seq
* @return
*/
- public abstract Color findColour(char symbol, int position,
+ Color findColour(char symbol, int position,
SequenceI seq);
- public abstract ColourSchemeI getColourScheme();
+ ColourSchemeI getColourScheme();
- public abstract void setColourScheme(ColourSchemeI cs);
+ void setColourScheme(ColourSchemeI cs);
}
\ No newline at end of file
package jalview.renderer;
import jalview.api.AlignViewportI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
/**
column = col;
text = txt;
}
-
- /**
- * String representation for inspection when debugging only
- */
- @Override
- public String toString()
- {
- return String.format("%s:%d:%s", major ? "major" : "minor", column,
- text);
- }
}
/**
- * Calculates position markers on the alignment ruler
+ * calculate positions markers on the alignment ruler
*
* @param av
* @param startx
- * left-most column in visible view (0..)
+ * left-most column in visible view
* @param endx
- * - right-most column in visible view (0..)
- * @return
+ * - right-most column in visible view
+ * @return List of ScaleMark holding boolean: true/false for major/minor mark,
+ * marker position in alignment column coords, a String to be rendered
+ * at the position (or null)
*/
public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
int endx)
int scalestartx = (startx / 10) * 10;
SequenceI refSeq = av.getAlignment().getSeqrep();
- int refSp = 0, refStartI = 0, refEndI = -1;
+ int refSp = 0;
+ int refStartI = 0;
+ int refEndI = -1;
+
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+
if (refSeq != null)
{
- // find bounds and set origin appopriately
- // locate first visible position for this sequence
- int[] refbounds = av.getAlignment().getHiddenColumns()
- .locateVisibleBoundsOfSequence(refSeq);
+ // find bounds and set origin appropriately
+ // locate first residue in sequence which is not hidden
+ Iterator<int[]> it = hc.iterator();
+ int index = refSeq.firstResidueOutsideIterator(it);
+ refSp = hc.absoluteToVisibleColumn(index);
+
+ refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+ int seqlength = refSeq.getLength();
+ // get sequence position past the end of the sequence
+ int pastEndPos = refSeq.findPosition(seqlength + 1);
+ refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
- refSp = refbounds[0];
- refStartI = refbounds[4];
- refEndI = refbounds[5];
scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
}
{
scalestartx += 5;
}
- List<ScaleMark> marks = new ArrayList<ScaleMark>();
+ List<ScaleMark> marks = new ArrayList<>();
+ String string;
+ int refN, iadj;
// todo: add a 'reference origin column' to set column number relative to
for (int i = scalestartx; i <= endx; i += 5)
{
if (((i - refSp) % 10) == 0)
{
- String text;
if (refSeq == null)
{
- int iadj = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(i - 1) + 1;
- text = String.valueOf(iadj);
+ iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
+ string = String.valueOf(iadj);
}
else
{
- int iadj = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(i - 1);
- int refN = refSeq.findPosition(iadj);
+ iadj = hc.visibleToAbsoluteColumn(i - 1);
+ refN = refSeq.findPosition(iadj);
// TODO show bounds if position is a gap
// - ie L--R -> "1L|2R" for
// marker
if (iadj < refStartI)
{
- text = String.valueOf(iadj - refStartI);
+ string = String.valueOf(iadj - refStartI);
}
else if (iadj > refEndI)
{
- text = "+" + String.valueOf(iadj - refEndI);
+ string = "+" + String.valueOf(iadj - refEndI);
}
else
{
- text = String.valueOf(refN) + refSeq.getCharAt(iadj);
+ string = String.valueOf(refN) + refSeq.getCharAt(iadj);
}
}
- marks.add(new ScaleMark(true, i - startx - 1, text));
+ marks.add(new ScaleMark(true, i - startx - 1, string));
}
else
{
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * Base class for colour schemes based on a selected Hidden Markov Model. The
+ * colour is with reference to an HMM consensus sequence and HMM profile
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion (position is gapped in the HMM consensus)</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ * where information content is the log ratio
+ *
+ * <pre>
+ * log(profile match emission probability / residue background probability)
+ * </pre>
+ *
+ * Sub-class implementations use either global ('Uniprot') or local
+ * ('alignment') background frequencies.
+ *
+ * @author tzvanaalten
+ * @author gmcarstairs
+ */
+public abstract class HmmerColourScheme extends ResidueColourScheme
+{
+ private static final Color INSERTION_COLOUR = new Color(230, 0, 0); // reddish
+
+ /*
+ * the aligned HMM consensus sequence to use as reference for colouring
+ */
+ private SequenceI hmmSeq;
+
+ private HiddenMarkovModel hmm;
+
+ private Map<Character, Float> frequencies;
+
+ /**
+ * Constructor given a Hidden Markov Model consensus sequence. This provides
+ * the HMM profile from which we can read the emission probabilities that
+ * determine the colour.
+ *
+ * @param consensusSeq
+ */
+ public HmmerColourScheme(SequenceI consensusSeq)
+ {
+ hmmSeq = consensusSeq;
+ hmm = hmmSeq == null ? null : hmmSeq.getHMM();
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HmmerColourScheme()
+ {
+ }
+
+ @Override
+ public Color findColour(char symbol, int column, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ return findColour(symbol, column);
+ }
+
+ /**
+ * Returns the colour at a particular symbol at a column in the alignment:
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ *
+ * @param symbol
+ * @param column
+ * @return
+ */
+ private Color findColour(char symbol, int column)
+ {
+ if (getHmm() == null || Comparison.isGap(symbol))
+ {
+ return Color.white;
+ }
+ if (Comparison.isGap(hmmSeq.getCharAt(column)))
+ {
+ return INSERTION_COLOUR;
+ }
+ if (Character.isLowerCase(symbol))
+ {
+ symbol = Character.toUpperCase(symbol);
+ }
+
+ final double prob = getHmm().getMatchEmissionProbability(column,
+ symbol);
+
+ Float freq = 0f;
+
+ if (!frequencies.containsKey(symbol))
+ {
+ return Color.WHITE;
+ }
+ else
+ {
+ freq = frequencies.get(symbol);
+ }
+
+ /*
+ * Orange if match emission probability is less than background probability
+ */
+ double infoRatio = prob / freq.floatValue();
+ Color colour = Color.ORANGE;
+ if (infoRatio >= 1)
+ {
+ /*
+ * log-scale graduated shade of blue if prob is greater than background
+ */
+ float infoLog = (float) Math.log(infoRatio);
+ colour = ColorUtils.getGraduatedColour(infoLog, 0, Color.WHITE,
+ getMaxInformationScore(), Color.blue);
+ }
+
+ return colour;
+ }
+
+ /**
+ * Answers the maximum possible value of information score (log ratio), for
+ * use in scaling a graduated colour range
+ *
+ * @return
+ */
+ abstract float getMaxInformationScore();
+
+ /**
+ * Answers a new colour scheme instance based on the HMM of the first sequence
+ * in ac that has an HMM
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI ac,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ return newInstance(ac);
+ }
+
+ /**
+ * Answers a new instance of the colour scheme for the given HMM
+ *
+ * @param ac
+ * @return
+ */
+ protected abstract HmmerColourScheme newInstance(AnnotatedCollectionI ac);
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+
+ /**
+ * Answers true if the sequence collection has an HMM consensus sequence, else
+ * false
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ return ac.getHmmConsensus() != null;
+ }
+
+ protected Map<Character, Float> getFrequencies()
+ {
+ return frequencies;
+ }
+
+ protected void setFrequencies(Map<Character, Float> frequencies)
+ {
+ this.frequencies = frequencies;
+ }
+
+ protected HiddenMarkovModel getHmm()
+ {
+ return hmm;
+ }
+
+ protected SequenceI getHmmSequence()
+ {
+ return hmmSeq;
+ }
+}
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * An HMM colour scheme that uses global ('Uniprot') background frequencies for
+ * residues
+ *
+ * @author tzvanaalten
+ */
+public class HmmerGlobalBackground extends HmmerColourScheme
+{
+ /*
+ * The highest possible log ratio is when match emission probability in
+ * the HMM model is 1, and background (for W) is 0.0109 giving
+ * log(1/0.0109) = log(91.743) = 4.519
+ */
+ private static final float MAX_LOG_RATIO = 4.519f;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param markov
+ */
+ public HmmerGlobalBackground(AnnotatedCollectionI ac)
+ {
+ super(ac.getHmmConsensus());
+ String alphabetType = getHmm() == null
+ ? ResidueProperties.ALPHABET_AMINO
+ : getHmm().getAlphabetType();
+ setFrequencies(
+ ResidueProperties.backgroundFrequencies.get(alphabetType));
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HmmerGlobalBackground()
+ {
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERU.toString();
+ }
+
+ @Override
+ protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
+ {
+ return new HmmerGlobalBackground(ac);
+ }
+
+ @Override
+ float getMaxInformationScore()
+ {
+ return MAX_LOG_RATIO;
+ }
+
+}
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * An HMM colour scheme that uses local (alignment or sub-group) background
+ * frequencies for residues
+ *
+ * @author tzvanaalten
+ */
+public class HmmerLocalBackground extends HmmerColourScheme
+{
+ float logTotalCount;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param sg
+ *
+ * @param markov
+ */
+ public HmmerLocalBackground(AnnotatedCollectionI ac)
+ {
+ super(ac.getHmmConsensus());
+ countFrequencies(ac);
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HmmerLocalBackground()
+ {
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERA.toString();
+ }
+
+ /**
+ * Counts and stores the relative frequency of every residue in the alignment
+ * (apart from any HMM consensus sequences)
+ *
+ * @param sg
+ */
+ public void countFrequencies(AnnotatedCollectionI sg)
+ {
+ // TODO or total counts in Consensus Profile (how do we get at it?)?
+ Map<Character, Float> freqs = new HashMap<>();
+
+ /*
+ * count symbols, excluding any HMM consensus sequences
+ */
+ ResidueCount counts = new ResidueCount();
+ List<SequenceI> seqs = sg.getSequences();
+ for (SequenceI seq : seqs)
+ {
+ if (!seq.isHMMConsensusSequence())
+ {
+ for (char c : seq.getSequence())
+ {
+ counts.add(c);
+ }
+ }
+ }
+ int total = counts.getTotalResidueCount(); // excludes gaps
+
+ for (char symbol : counts.getSymbolCounts().symbols)
+ {
+ double freq = counts.getCount(symbol) / (double) total;
+ freqs.put(symbol, (float) freq);
+ }
+
+ setFrequencies(freqs);
+
+ logTotalCount = (float) Math.log(total);
+ }
+
+ @Override
+ float getMaxInformationScore()
+ {
+ return logTotalCount;
+ }
+
+ @Override
+ protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
+ {
+ return new HmmerLocalBackground(ac);
+ }
+}
Nucleotide("Nucleotide", NucleotideColourScheme.class),
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
- TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
+ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+ HMMERU("HMMER-Uniprot", HmmerGlobalBackground.class),
+ HMMERA("HMMER-Alignment", HmmerLocalBackground.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
public class ResidueProperties
{
+ // alphabet names used in Hidden Markov Model files
+ public static final String ALPHABET_RNA = "RNA";
+
+ public static final String ALPHABET_DNA = "DNA";
+
+ public static final String ALPHABET_AMINO = "amino";
+
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
public static final Map<String, String> modifications = new HashMap<>();
+ // residue background frequencies across different alphabets
+ public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
+
static
{
aaIndex = new int[255];
}
+ static
+ {
+ Map<Character, Float> amino = new HashMap<>();
+ amino.put('A', 0.0826f);
+ amino.put('Q', 0.0393f);
+ amino.put('L', 0.0965f);
+ amino.put('S', 0.0661f);
+ amino.put('R', 0.0553f);
+ amino.put('E', 0.0674f);
+ amino.put('K', 0.0582f);
+ amino.put('T', 0.0535f);
+ amino.put('N', 0.0406f);
+ amino.put('G', 0.0708f);
+ amino.put('M', 0.0241f);
+ amino.put('W', 0.0109f);
+ amino.put('D', 0.0546f);
+ amino.put('H', 0.0227f);
+ amino.put('F', 0.0386f);
+ amino.put('Y', 0.0292f);
+ amino.put('C', 0.0137f);
+ amino.put('I', 0.0593f);
+ amino.put('P', 0.0472f);
+ amino.put('V', 0.0686f);
+ backgroundFrequencies.put(ALPHABET_AMINO, amino);
+ // todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
+ // are they?
+ }
+
+ // TODO get correct frequencies
+
+ static
+ {
+ Map<Character, Float> dna = new HashMap<>();
+ dna.put('A', 0.25f);
+ dna.put('C', 0.25f);
+ dna.put('T', 0.25f);
+ dna.put('G', 0.25f);
+ backgroundFrequencies.put(ALPHABET_DNA, dna);
+
+ }
+
+ static
+ {
+ Map<Character, Float> rna = new HashMap<>();
+ rna.put('A', 0.25f);
+ rna.put('C', 0.25f);
+ rna.put('T', 0.25f);
+ rna.put('G', 0.25f);
+ backgroundFrequencies.put(ALPHABET_RNA, rna);
+
+ }
+
public static String getCanonicalAminoAcid(String aA)
{
String canonical = modifications.get(aA);
package jalview.structure;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import java.util.ArrayList;
String pdbchain;
- public static final int UNASSIGNED_VALUE = -1;
+ public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
private static final int PDB_RES_NUM_INDEX = 0;
// and atomNo
HashMap<Integer, int[]> mapping;
+ jalview.datamodel.Mapping seqToPdbMapping = null;
/**
* Constructor
*
this.mappingDetails = mappingDetails;
}
+ public StructureMapping(SequenceI seq, String pdbFile2, String pdbId2,
+ String chain, HashMap<Integer, int[]> mapping2,
+ String mappingOutput, Mapping seqToPdbMapping)
+ {
+ this(seq, pdbFile2, pdbId2, chain, mapping2, mappingOutput);
+ this.seqToPdbMapping = seqToPdbMapping;
+ }
+
public SequenceI getSequence()
{
return sequence;
/**
*
* @param seqpos
- * @return 0 or the corresponding residue number for the sequence position
+ * @return UNASSIGNED_VALUE or the corresponding residue number for the
+ * sequence position
*/
public int getPDBResNum(int seqpos)
{
{
return mapping;
}
+
+ public Mapping getSeqToPdbMapping()
+ {
+ return seqToPdbMapping;
+ }
}
private boolean addTempFacAnnot = false;
- private SiftsClient siftsClient = null;
-
/*
* Set of any registered mappings between (dataset) sequences.
*/
}
/**
- * create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
+ * Import a single structure file and register sequence structure mappings for
+ * broadcasting colouring, mouseovers and selection events (convenience
+ * wrapper).
*
* @param forStructureView
* when true, record the mapping for use in mouseOvers
- *
- * @param sequenceArray
+ * @param sequence
* - one or more sequences to be mapped to pdbFile
- * @param targetChainIds
+ * @param targetChains
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
- * - this should be List<List<String>>, empty lists indicate no
- * predefined mappings
+ * (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
- * @param sourceType
+ * @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
pdbFile, sourceType, null);
}
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol). Either constructs a mapping
+ * using NW alignment or derives one from any available SIFTS mapping data.
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequenceArray
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChainIds
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
+ * @param pdbFile
+ * - structure data resource
+ * @param sourceType
+ * - how to resolve data from resource
+ * @param IProgressIndicator
+ * reference to UI component that maintains a progress bar for the
+ * mapping operation
+ * @return null or the structure data parsed as a pdb file
+ */
synchronized public StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
String[] targetChainIds, String pdbFile, DataSourceType sourceType,
IProgressIndicator progress)
{
long progressSessionId = System.currentTimeMillis() * 3;
- /*
- * There will be better ways of doing this in the future, for now we'll use
- * the tried and tested MCview pdb mapping
+
+ /**
+ * do we extract and transfer annotation from 3D data ?
*/
- boolean parseSecStr = processSecondaryStructure;
- if (isPDBFileRegistered(pdbFile))
- {
- for (SequenceI sq : sequenceArray)
- {
- SequenceI ds = sq;
- while (ds.getDatasetSequence() != null)
- {
- ds = ds.getDatasetSequence();
- }
- ;
- if (ds.getAnnotation() != null)
- {
- for (AlignmentAnnotation ala : ds.getAnnotation())
- {
- // false if any annotation present from this structure
- // JBPNote this fails for jmol/chimera view because the *file* is
- // passed, not the structure data ID -
- if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
- {
- parseSecStr = false;
- }
- }
- }
- }
- }
+ // FIXME: possibly should just delete
+
+ boolean parseSecStr = processSecondaryStructure
+ ? isStructureFileProcessed(pdbFile, sequenceArray)
+ : false;
+
StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
+ // FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(pdbFile, sourceType);
ex.printStackTrace();
return null;
}
-
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
try
{
if (isMapUsingSIFTs)
{
isMapUsingSIFTs = false;
e.printStackTrace();
+ siftsClient = null;
}
String targetChainId;
try
{
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ maxChain.makeExactMapping(siftsMapping, seq);
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
// "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ // this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
+ StructureMapping siftsMapping = null;
try
{
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ siftsMapping = getStructureMapping(seq,
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+ siftsClient);
foundSiftsMappings.add(siftsMapping);
+ chain.makeExactMapping(siftsMapping, seq);
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ // "IEA:SIFTS" ?
+ chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
if (!foundSiftsMappings.isEmpty())
{
seqToStrucMapping.addAll(foundSiftsMappings);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
- // "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
- sqmpping);
ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
return pdb;
}
+ /**
+ * check if we need to extract secondary structure from given pdbFile and
+ * transfer to sequences
+ *
+ * @param pdbFile
+ * @param sequenceArray
+ * @return
+ */
+ private boolean isStructureFileProcessed(String pdbFile,
+ SequenceI[] sequenceArray)
+ {
+ boolean parseSecStr = true;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
+ }
+ return parseSecStr;
+ }
+
public void addStructureMapping(StructureMapping sm)
{
mappings.add(sm);
* @param maxChain
* @param sqmpping
* @param maxAlignseq
+ * @param siftsClient
+ * client for retrieval of SIFTS mappings for this structure
* @return
* @throws SiftsException
*/
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
+ AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ chain.transferResidueAnnotation(curChainMapping, null);
}
} catch (Exception e)
{
--- /dev/null
+package jalview.util;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Scanner;
+import java.util.Vector;
+
+/**
+ * Processes probability data. The file indexes used in this program represent
+ * the index of the location of a family or hmm in their respective files,
+ * starting from 0.
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMProbabilityDistributionAnalyser
+{
+ AlignmentAnnotation reference = null;
+
+ Vector<SequenceI> sequences;
+
+ HiddenMarkovModel hmm;
+
+ // contains the raw data produced
+ List<ArrayList<Double>> raw = new ArrayList<>();
+
+ // contains binned data
+ Map<String, Double> binned = new HashMap<>();
+
+ // location of the family file
+ String families = "/media/sf_Shared_Folder/PFAM/Family/SeedFamilies.seed";
+
+ // location of the file containing the family-clan links
+ final static String FAMILIESTOCLAN = "/media/sf_Shared_Folder/PFAM/Family/Clanlinks.dat";
+
+ // location of the HMM file
+ String hmms = "/media/sf_Shared_Folder/PFAM/HMMs/Pfam-A.hmm";
+
+ // suffix for raw file
+ final static String RAW = "/Raw.csv";
+
+ // suffix for binned file
+ final static String BINNED = "/Binned.csv";
+
+ // normalisation scale
+ final static double SCALE = 1;
+
+ // current position in file
+ int currentFilePosition = 0;
+
+ final static String NL = "\n";
+
+ Random generator = new Random();
+
+ // current directory
+ String currentFolder;
+
+ boolean keepRaw = false;
+
+ /**
+ * Sets the working directory.
+ *
+ * @param path
+ */
+ public void setFolder(String path)
+ {
+ currentFolder = path;
+ }
+
+ /**
+ * Moves a buffered reader forward in the file by a certain amount of entries.
+ * Each entry in the file is delimited by '//'.
+ *
+ * @param index
+ * The index of the location in the file.
+ * @param br
+ * @throws IOException
+ */
+ public void moveLocationBy(int index, BufferedReader br)
+ throws IOException
+ {
+ for (int i = 0; i < index; i++)
+ {
+ String line = br.readLine();
+ while (!"//".equals(line))
+ {
+ line = br.readLine();
+
+ }
+ }
+
+ }
+
+ /**
+ * Analyses a specified number of families and then saves the data. Before
+ * analysing the data, the previous saved data will be imported and after
+ * analysing this, the data is exported back into the file. The file must be
+ * in flat file format.
+ *
+ * @param increments
+ * The number of families to read before saving.
+ * @throws IOException
+ */
+ public void run(int increments, boolean keepRawData) throws IOException
+ {
+ keepRaw = keepRawData;
+ try
+ {
+ readPreviousData(currentFolder);
+ BufferedReader posReader = new BufferedReader(
+ new FileReader(currentFolder + "/CurrentPosition.txt"));
+
+ String line = posReader.readLine();
+ posReader.close();
+ currentFilePosition = Integer.parseInt(line);
+ } catch (Exception e)
+ {
+ System.out.println("No previous data found");
+ }
+
+
+
+ BufferedReader inputSTO = new BufferedReader(new FileReader(families));
+ BufferedReader inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+
+ moveLocationBy(currentFilePosition, inputHMM);
+ moveLocationBy(currentFilePosition, inputSTO);
+
+ int filesRead = 0;
+ int i = 0;
+ while (filesRead < increments)
+ {
+
+ readStockholm(inputSTO);
+
+ readHMM(inputHMM);
+
+ int count = countValidResidues();
+ processData(count);
+ filesRead++;
+
+ currentFilePosition++;
+ System.out.println(i);
+ i++;
+ }
+
+ PrintWriter p = new PrintWriter(
+ new File(currentFolder + "/CurrentPosition.txt"));
+ p.print(currentFilePosition);
+ p.close();
+ exportData(currentFolder);
+ raw.clear();
+ binned.clear();
+
+ }
+
+ /**
+ * Analyses all families and then saves the data. Before analysing the data,
+ * the previous saved data will be imported and after analysing this, the data
+ * is exported back into the file. The file must be in flat file format.
+ *
+ * @param increments
+ * The number of families to read before saving.
+ * @throws IOException
+ */
+ public void runToEnd(int minCount, int maxCount, boolean keepRawData,
+ boolean forClans)
+ throws IOException
+ {
+ keepRaw = keepRawData;
+ BufferedReader inputSTO = null;
+ BufferedReader inputHMM = null;
+ int size = 0;
+ int files = 1;
+ try
+ {
+ if (forClans)
+ {
+ files = 603;
+ }
+ int filesRead = 0;
+ for (int clan = 0; clan < files; clan++)
+ {
+ System.out.println(clan);
+ String clanPath = "";
+ int numberOfFamilies = 0;
+ if (forClans)
+ {
+ clanPath = currentFolder + "/Clan" + clan;
+ if (!new File(clanPath).exists())
+ {
+ continue;
+ }
+ BufferedReader famCountReader = new BufferedReader(
+ new FileReader(clanPath + "/NumberOfFamilies.txt"));
+ numberOfFamilies = Integer.parseInt(famCountReader.readLine());
+ }
+ else
+ {
+ numberOfFamilies = 1;
+ }
+
+ for (int fam = 0; fam < numberOfFamilies; fam++)
+ {
+ if (forClans)
+ {
+ families = clanPath + "/Families/Fam" + fam + ".sto";
+ hmms = clanPath + "/HMMs/HMM" + fam + ".hmm";
+ }
+
+ inputSTO = new BufferedReader(new FileReader(families));
+ inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+ int i = 0;
+ boolean endReached = atEnd(inputSTO);
+ while (!endReached)
+ {
+ readStockholm(inputSTO);
+ readHMM(inputHMM);
+
+ int count = countValidResidues();
+ if (count >= minCount && count < maxCount)
+ {
+ processData(count);
+ }
+ filesRead++;
+ System.out.println(filesRead);
+ endReached = atEnd(inputSTO);
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ exportData(currentFolder);
+ raw.clear();
+ binned.clear();
+ }
+ }
+
+ /**
+ * Reads the previous data from both files
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readPreviousData(String source) throws IOException
+ {
+ readBinned(source);
+ if (keepRaw)
+ {
+ readRaw(source);
+ }
+ }
+
+ /**
+ * Reads the previous data from the binned file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readBinned(String source) throws IOException
+ {
+ BufferedReader input = new BufferedReader(
+ new FileReader(source + BINNED));
+ String line = input.readLine();
+ binned = new HashMap<>();
+ while (!("".equals(line) || line == null))
+ {
+ Scanner scanner = new Scanner(line);
+ scanner.useDelimiter(",");
+ String key = scanner.next();
+ String value = scanner.next();
+ binned.put(key, Double.valueOf(value));
+ scanner.close();
+ line = input.readLine();
+ }
+
+ input.close();
+ }
+
+ /**
+ * Reads the previous data from the raw file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readRaw(String source) throws IOException
+ {
+ BufferedReader input = new BufferedReader(new FileReader(source + RAW));
+ String line = input.readLine();
+ if (line == null)
+ {
+ input.close();
+ return;
+ }
+ Scanner numberScanner = new Scanner(line);
+ numberScanner.useDelimiter(",");
+ raw = new ArrayList<>();
+ while (numberScanner.hasNext())
+ {
+ numberScanner.next();
+ raw.add(new ArrayList<Double>());
+ }
+ numberScanner.close();
+
+ line = input.readLine();
+ while (!("".equals(line) || line == null))
+ {
+ Scanner scanner = new Scanner(line);
+ scanner.useDelimiter(",");
+
+ int i = 0;
+ while (scanner.hasNext())
+ {
+ String value;
+ value = scanner.next();
+ if (!value.equals("EMPTY"))
+ {
+ raw.get(i).add(Double.parseDouble(value));
+ }
+ else
+ {
+ raw.get(i).add(null);
+ }
+
+ i++;
+ }
+ scanner.close();
+ line = input.readLine();
+ }
+
+ input.close();
+ }
+
+ /**
+ * Counts the number of valid residues in the sequence.
+ *
+ * @return
+ */
+ public int countValidResidues()
+ {
+ int count = 0;
+
+ for (int width = 0; width < sequences.size(); width++)
+ {
+ for (int length = 1; length < hmm.getLength() + 1; length++)
+ {
+ char symbol;
+ int alignPos;
+ alignPos = hmm.getNodeMapPosition(length);
+
+ symbol = sequences.get(width).getCharAt(alignPos);
+ if (ResidueProperties.backgroundFrequencies.get("amino")
+ .containsKey(symbol))
+ {
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+
+ /**
+ * Processes data, and stores it in both a raw and binned format.
+ *
+ * @param count
+ */
+ public void processData(int count)
+ {
+ int rawPos = 0;
+ if (keepRaw)
+ {
+ raw.add(new ArrayList<Double>());
+ rawPos = raw.size() - 1;
+ }
+ Double total = 0d;
+ for (int width = 0; width < sequences.size(); width++)
+ {
+ for (int length = 1; length < hmm.getLength() + 1; length++)
+ {
+ char symbol;
+ int alignPos;
+ alignPos = hmm.getNodeMapPosition(length);
+
+ symbol = sequences.get(width).getCharAt(alignPos);
+ if (ResidueProperties.backgroundFrequencies.get("amino")
+ .containsKey(symbol))
+ {
+ Double prob;
+ Float bfreq;
+ Double llr;
+ prob = hmm.getMatchEmissionProbability(alignPos, symbol);
+ bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+ .get(symbol);
+ if (prob == 0 || bfreq == 0)
+ {
+ System.out.println("error");
+ }
+ llr = Math.log(prob / bfreq);
+ if (keepRaw)
+ {
+ raw.get(rawPos).add(llr);
+ }
+
+ String output;
+ output = String.format("%.1f", llr);
+ total += Double.parseDouble(output);
+ if ("-0.0".equals(output))
+ {
+ output = "0.0";
+ }
+ if (binned.containsKey(output))
+ {
+ double prev = binned.get(output);
+ prev += (SCALE / count);
+ binned.put(output, prev);
+
+ }
+ else
+ {
+ binned.put(output, SCALE / count);
+ }
+ }
+ }
+ }
+ System.out.println(total / count);
+ }
+
+
+ /**
+ * Reads in the sequence data from a Stockholm file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readStockholm(BufferedReader inputSTO) throws IOException
+ {
+ FileParse parserSTO = new FileParse(inputSTO, "", DataSourceType.FILE);
+ StockholmFile file = new StockholmFile(parserSTO);
+ Vector<AlignmentAnnotation> annots = file.getAnnotations();
+
+ for (AlignmentAnnotation annot : annots)
+ {
+ if (annot.label.contains("Reference"))
+ {
+ reference = annot;
+ }
+ }
+ sequences = file.getSeqs();
+ }
+
+ /**
+ * Reads in the HMM data from a HMMer file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readHMM(BufferedReader inputHMM) throws IOException
+ {
+ FileParse parserHMM = new FileParse(inputHMM, "", DataSourceType.FILE);
+ HMMFile file = new HMMFile(parserHMM);
+ hmm = file.getHMM();
+
+
+ }
+
+ /**
+ * Exports both the binned and raw data into separate files.
+ *
+ * @param location
+ * @throws FileNotFoundException
+ */
+ public void exportData(String location) throws FileNotFoundException
+ {
+ PrintWriter writerBin = new PrintWriter(new File(location + BINNED));
+ for (Map.Entry<String, Double> entry : binned.entrySet())
+ {
+ writerBin.println(entry.getKey() + "," + entry.getValue());
+ }
+ writerBin.close();
+ if (keepRaw)
+ {
+
+ PrintWriter writerRaw = new PrintWriter(new File(location + RAW));
+
+ StringBuilder identifier = new StringBuilder();
+
+ for (int i = 1; i < raw.size() + 1; i++)
+ {
+ identifier.append("Fam " + i + ",");
+ }
+
+ writerRaw.println(identifier);
+
+ boolean rowIsEmpty = false;
+ int row = 0;
+ while (!rowIsEmpty)
+ {
+ rowIsEmpty = true;
+ StringBuilder string = new StringBuilder();
+ for (int column = 0; column < raw.size(); column++)
+ {
+ if (raw.get(column).size() <= row)
+ {
+ string.append("EMPTY,");
+ }
+ else
+ {
+ string.append(raw.get(column).get(row) + ",");
+ rowIsEmpty = false;
+ }
+ }
+ row++;
+ writerRaw.println(string);
+ }
+ writerRaw.close();
+
+ }
+
+ }
+
+ /**
+ * Prints the specified family on the console.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void printFam(int index) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(families));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ while (!"//".equals(line))
+ {
+ System.out.println(line);
+ line = br.readLine();
+ }
+ System.out.println(line);
+ br.close();
+
+ }
+
+ /**
+ * Prints the specified HMM on the console.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void printHMM(int index) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ while (!"//".equals(line))
+ {
+ System.out.println(line);
+ line = br.readLine();
+ }
+ System.out.println(line);
+ br.close();
+
+ }
+
+ /**
+ * Prints the specified family to a .sto file.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void exportFam(int index, String location) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(families));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(new File(location), true));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+ br.close();
+
+ }
+
+ public void exportFile(BufferedReader br, String location, boolean append)
+ throws IOException
+ {
+ String line = br.readLine();
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(location, append));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+
+
+ }
+
+ public String getHMMName(int index) throws IOException
+ {
+ String name;
+
+ BufferedReader nameFinder = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, nameFinder);
+
+ nameFinder.readLine();
+
+ Scanner scanner = new Scanner(nameFinder.readLine());
+ name = scanner.next();
+ name = scanner.next();
+ scanner.close();
+ return name;
+ }
+
+ public String getFamilyName(int index) throws IOException
+ {
+ String name;
+
+ BufferedReader nameFinder = new BufferedReader(
+ new FileReader(families));
+
+ moveLocationBy(index, nameFinder);
+
+ nameFinder.readLine();
+
+ Scanner scanner = new Scanner(nameFinder.readLine());
+ name = scanner.next();
+ name = scanner.next();
+ name = scanner.next();
+ scanner.close();
+ return name;
+ }
+
+ /**
+ * Prints the specified family to a .hmm file.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void exportHMM(int index, String location) throws IOException
+ {
+
+
+ BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(new File(location), true));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+ br.close();
+
+ }
+
+ /**
+ * Clears all raw, binned and current position data in the current directory.
+ *
+ * @throws FileNotFoundException
+ */
+ public void clear() throws FileNotFoundException
+ {
+ PrintWriter pos = new PrintWriter(
+ currentFolder + "/CurrentPosition.txt");
+ pos.println("0");
+
+ PrintWriter raw = new PrintWriter(currentFolder + RAW);
+
+ PrintWriter bin = new PrintWriter(currentFolder + BINNED);
+
+ pos.close();
+ bin.close();
+ raw.close();
+ }
+
+ public void sortIntoClans(String directory) throws IOException
+ {
+ BufferedReader clanFinder = new BufferedReader(new FileReader(FAMILIESTOCLAN));
+ BufferedReader familyReader = new BufferedReader(
+ new FileReader(families));
+ BufferedReader hmmReader = new BufferedReader(new FileReader(hmms));
+ int families = 0;
+ // moveLocationBy(7000, familyReader);
+ // moveLocationBy(7000, clanFinder);
+ // moveLocationBy(7000, hmmReader);
+ HashMap<String, Integer> clanIndexes = new HashMap<>();
+ ArrayList<Integer> familyCounts = new ArrayList<>();
+ int filePos = 0;
+ int clanCount = 0;
+ String line;
+ line = clanFinder.readLine();
+
+ while (!"".equals(line) && !" ".equals(line) && line != null)
+ {
+ String clanName;
+ boolean inClan = false;
+ while (!(line.indexOf("//") > -1))
+ {
+
+ if (line.indexOf("#=GF CL") > -1)
+ {
+ families++;
+ System.out.println(families);
+ inClan = true;
+ Scanner scanner = new Scanner(line);
+ scanner.next();
+ scanner.next();
+ clanName = scanner.next();
+ scanner.close();
+
+ if (!clanIndexes.containsKey(clanName))
+ {
+ clanIndexes.put(clanName, clanCount);
+ clanCount++;
+ familyCounts.add(0);
+ }
+
+
+ Integer clanI = clanIndexes.get(clanName);
+ String clanPath = directory + "/Clan" + clanI.toString();
+ createFolders(clanPath);
+
+ int index = clanIndexes.get(clanName);
+ exportFile(familyReader,
+ clanPath + "/Families/Fam" + familyCounts.get(index)
+ + ".sto",
+ false);
+ exportFile(hmmReader,
+ clanPath + "/HMMs/HMM" + familyCounts.get(index) + ".hmm",
+ false);
+
+ int count = familyCounts.get(index);
+ count++;
+ familyCounts.set(index, count);
+ }
+ line = clanFinder.readLine();
+
+ }
+ if (!inClan)
+ {
+ moveLocationBy(1, familyReader);
+ moveLocationBy(1, hmmReader);
+ }
+ filePos++;
+ // System.out.println(filePos + " files read.");
+ line = clanFinder.readLine();
+
+ }
+ clanFinder.close();
+
+ for (int clan = 0; clan < clanCount; clan++)
+ {
+ PrintWriter writer = new PrintWriter(
+ directory + "/Clan" + clan + "/NumberOfFamilies.txt");
+ int count = familyCounts.get(clan);
+ writer.print(count);
+ writer.close();
+ }
+
+ }
+
+ public String getFamilies()
+ {
+ return families;
+ }
+
+ public void setFamilies(String families)
+ {
+ this.families = currentFolder + families;
+ }
+
+ public String getHmms()
+ {
+ return hmms;
+ }
+
+ public void setHmms(String hmms)
+ {
+ this.hmms = currentFolder + hmms;
+ }
+
+ public void alignWithinClan(String exportLocation, String clansLocation)
+ throws IOException, InterruptedException
+ {
+ int alignmentsExported = 0;
+ for (int clan = 0; clan < 604; clan++)
+ {
+ System.out.println(clan);
+ int famCount = 0;
+ String clanPath = clansLocation + "/Clan" + clan;
+ int numberOfFamilies;
+ BufferedReader br = new BufferedReader(
+ new FileReader(clanPath + "/NumberOfFamilies.txt"));
+ String line = br.readLine();
+ numberOfFamilies = Integer.parseInt(line);
+ br.close();
+ if (numberOfFamilies == 1)
+ {
+ continue;
+ }
+ final String commandExportLocation = exportLocation + "/Clan" + clan;
+ createFolders(commandExportLocation);
+ for (int family = 0; family < numberOfFamilies; family++)
+ {
+ famCount++;
+ ArrayList<Integer> indexes = new ArrayList<>();
+ for (int i = 0; i < numberOfFamilies; i++)
+ {
+ if (i != family)
+ {
+ indexes.add(i);
+ }
+ }
+
+ int hmmIndex = getRandom(indexes);
+ String famPath = clanPath + "/Families/Fam" + family + ".sto";
+ String hmmPath = clanPath + "/HMMs/HMM" + hmmIndex + ".hmm";
+ String command = "/media/sf_Shared_Folder/hmmer/binaries/hmmalign --mapali "
+ + clanPath + "/Families/Fam" + hmmIndex + ".sto"
+ + " --trim ";
+ command += hmmPath + " ";
+ command += famPath;
+ final int familyIndex = family;
+ final Process p = Runtime.getRuntime().exec(command);
+
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BufferedReader input = new BufferedReader(
+ new InputStreamReader(p.getInputStream()));
+ String line = null;
+
+ try
+ {
+ PrintWriter writer = new PrintWriter(commandExportLocation
+ + "/Families/Fam" + familyIndex + ".sto");
+ String lastLine = "";
+ boolean dataFound = false;
+ while ((line = input.readLine()) != null)
+ {
+ if (line.contains("#=GR") && !dataFound)
+ {
+ writer.println(lastLine);
+ dataFound = true;
+ }
+ if (line.contains("#") || dataFound || " ".equals(line)
+ || "".equals(line) || "//".equals(line))
+ {
+ writer.println(line);
+ }
+ lastLine = line;
+ }
+ writer.close();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }).start();
+
+ p.waitFor();
+
+ BufferedReader hmmExporter = new BufferedReader(
+ new FileReader(hmmPath));
+
+ exportFile(hmmExporter,
+ commandExportLocation + "/HMMs/HMM" + family + ".hmm",
+ false);
+
+ alignmentsExported++;
+
+
+ }
+ PrintWriter writer = new PrintWriter(
+ commandExportLocation + "/NumberOfFamilies.txt");
+ writer.print(famCount);
+ writer.close();
+ }
+
+ }
+
+ public boolean atEnd(BufferedReader br) throws IOException
+ {
+ boolean end = false;
+ br.mark(80);
+ String line = br.readLine();
+ if ("".equals(line) || line == null)
+ {
+ end = true;
+ }
+ br.reset();
+ return end;
+ }
+
+ public int getRandom(ArrayList<Integer> list)
+ {
+ if (!(list.size() > 0))
+ {
+ System.out.println("Error - size = " + list.size());
+ }
+ int index = generator.nextInt(list.size());
+ int value = list.get(index);
+ list.remove(index);
+ return value;
+ }
+
+ public void createFolders(String clanPath)
+ {
+ File clanFolder = new File(clanPath);
+ if (!clanFolder.exists())
+ {
+ clanFolder.mkdir();
+ }
+
+ File famFolder = new File(clanPath + "/Families");
+ File hmmFolder = new File(clanPath + "/HMMs");
+ if (!famFolder.exists())
+ {
+ famFolder.mkdir();
+ hmmFolder.mkdir();
+ }
+ }
+}
+
+
+
+
for (int[] range : map.getFromRanges())
{
- addRange(range, fromShifts);
+ MappingUtils.addRange(range, fromShifts);
}
for (int[] range : map.getToRanges())
{
- addRange(range, toShifts);
+ MappingUtils.addRange(range, toShifts);
}
}
/**
- * Adds the given range to a list of ranges. If the new range just extends
- * existing ranges, the current endpoint is updated instead.
- *
- * @param range
- * @param addTo
- */
- static void addRange(int[] range, List<int[]> addTo)
- {
- /*
- * list is empty - add to it!
- */
- if (addTo.size() == 0)
- {
- addTo.add(range);
- return;
- }
-
- int[] last = addTo.get(addTo.size() - 1);
- boolean lastForward = last[1] >= last[0];
- boolean newForward = range[1] >= range[0];
-
- /*
- * contiguous range in the same direction - just update endpoint
- */
- if (lastForward == newForward && last[1] == range[0])
- {
- last[1] = range[1];
- return;
- }
-
- /*
- * next range starts at +1 in forward sense - update endpoint
- */
- if (lastForward && newForward && range[0] == last[1] + 1)
- {
- last[1] = range[1];
- return;
- }
-
- /*
- * next range starts at -1 in reverse sense - update endpoint
- */
- if (!lastForward && !newForward && range[0] == last[1] - 1)
- {
- last[1] = range[1];
- return;
- }
-
- /*
- * just add the new range
- */
- addTo.add(range);
- }
-
- /**
* Returns true if mapping is from forward strand, false if from reverse
* strand. Result is just based on the first 'from' range that is not a single
* position. Default is true unless proven to be false. Behaviour is not well
toSequences, fromGapChar);
}
- for (int[] hidden : hiddencols.getHiddenColumnsCopy())
+ Iterator<int[]> regions = hiddencols.iterator();
+ while (regions.hasNext())
{
- mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
+ mapHiddenColumns(regions.next(), codonFrames, newHidden,
+ fromSequences,
toSequences, fromGapChar);
}
return; // mappedColumns;
}
}
}
+
+ /**
+ * Adds the given range to a list of ranges. If the new range just extends
+ * existing ranges, the current endpoint is updated instead.
+ *
+ * @param range
+ * @param addTo
+ */
+ public static void addRange(int[] range, List<int[]> addTo)
+ {
+ /*
+ * list is empty - add to it!
+ */
+ if (addTo.size() == 0)
+ {
+ addTo.add(range);
+ return;
+ }
+
+ int[] last = addTo.get(addTo.size() - 1);
+ boolean lastForward = last[1] >= last[0];
+ boolean newForward = range[1] >= range[0];
+
+ /*
+ * contiguous range in the same direction - just update endpoint
+ */
+ if (lastForward == newForward && last[1] == range[0])
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * next range starts at +1 in forward sense - update endpoint
+ */
+ if (lastForward && newForward && range[0] == last[1] + 1)
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * next range starts at -1 in reverse sense - update endpoint
+ */
+ if (!lastForward && !newForward && range[0] == last[1] - 1)
+ {
+ last[1] = range[1];
+ return;
+ }
+
+ /*
+ * just add the new range
+ */
+ addTo.add(range);
+ }
}
--- /dev/null
+package jalview.util;
+
+import java.io.IOException;
+import java.util.Scanner;
+
+/**
+ * This class contains the brain of the analyser program, and contains a number
+ * of commands for the processing of data.
+ *
+ * @author TZVanaalten
+ *
+ */
+
+public class ProbabilityAnalyserKickstarter
+{
+
+ public static void main(String[] args)
+ throws IOException, InterruptedException
+ {
+
+ // this does all of the processing
+ HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+ boolean running = true;
+ System.out.println("ACTIVATED");
+ while (running)
+ {
+ Scanner keyboard = new Scanner(System.in);
+ String command = keyboard.nextLine();
+
+ Scanner inputScanner = new Scanner(command);
+ // prints family to console. Syntax is printFam <index>
+ if (command.indexOf("printFam") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ analyser.printFam(index);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+
+ }
+ // prints HMM to console. Syntax is printHMM <index>
+ if (command.indexOf("printHMM") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ analyser.printHMM(index);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // prints family to file in current folder. Syntax is exportFam <index>.
+ if (command.indexOf("exportFam") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ String location = inputScanner.next();
+ analyser.exportFam(index, location);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // prints HMM to file in current folder. Syntax is exportHMM <index>.
+ if (command.indexOf("exportHMM") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ String location = inputScanner.next();
+ analyser.exportHMM(index, location);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // Processes data. Syntax is run <number of loops> <increments>. The
+ // number loops specifies the number of increments the program will run.
+ // After each increment, the data stored currently in the program is
+ // exported and re-read back into the program. This is to ensure that the
+ // program can be terminated without losing a large quantity of data. The
+ // increment is the number of families read per 'save'.
+ if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
+ {
+ try
+ {
+
+ inputScanner.next();
+
+ int loops = inputScanner.nextInt();
+ int increments = inputScanner.nextInt();
+ boolean keepRaw = inputScanner.nextBoolean();
+
+ for (int i = 0; i < loops; i++)
+ {
+ analyser.run(increments, keepRaw);
+ System.out.println("Saved");
+ }
+ System.out.println("Task completed");
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ if ((command.indexOf("runToEnd") > -1))
+ {
+ try
+ {
+
+ inputScanner.next();
+ int minCount = inputScanner.nextInt();
+ int maxCount = inputScanner.nextInt();
+ boolean keepRaw = inputScanner.nextBoolean();
+ boolean forClans = inputScanner.nextBoolean();
+ analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
+ System.out.println("Task completed");
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ // terminates program. Syntax is terminate.
+ if (command.indexOf("terminate") > -1)
+ {
+ running = false;
+ continue;
+ }
+ // clears files in current directory (Only a specific set of files).
+ // Syntax is clear.
+ if (command.indexOf("clear") > -1)
+ {
+ analyser.clear();
+ continue;
+ }
+ // changes current directory. Syntax is cd <directory>
+ if (command.indexOf("cd") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ analyser.setFolder(inputScanner.next());
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+
+ }
+ continue;
+ }
+
+ if (command.indexOf("getFamName") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
+
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ if (command.indexOf("sortIntoClans") > -1)
+ {
+ inputScanner.next();
+ analyser.sortIntoClans(inputScanner.next());
+ continue;
+
+ }
+ if (command.indexOf("setFamilies") > -1)
+ {
+ inputScanner.next();
+ analyser.setFamilies(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("setHMMs") > -1)
+ {
+ inputScanner.next();
+ analyser.setHmms(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("alignWithinClans") > -1)
+ {
+ inputScanner.next();
+ String export = inputScanner.next();
+ String clans = inputScanner.next();
+ analyser.alignWithinClan(export, clans);
+ continue;
+
+ }
+
+ System.out.println("Unrecognised command");
+ }
+
+
+
+
+ }
+
+}
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
+import jalview.workers.InformationThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
import java.util.Deque;
import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
protected Deque<CommandI> redoList = new ArrayDeque<>();
+ protected String sequenceSetID;
+
+ /*
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
+
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+ protected ColumnSelection colSel = new ColumnSelection();
+
+ public boolean autoCalculateConsensus = true;
+
+ protected boolean autoCalculateStrucConsensus = true;
+
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+ protected boolean infoLetterHeight = false;
+
+ protected ResidueShaderI residueShading = new ResidueShader();
+
+ protected AlignmentAnnotation consensus;
+
+ protected AlignmentAnnotation complementConsensus;
+
+ protected AlignmentAnnotation occupancy;
+
+ protected AlignmentAnnotation strucConsensus;
+
+ protected AlignmentAnnotation conservation;
+
+ protected AlignmentAnnotation quality;
+
+ /**
+ * alignment displayed in the viewport
+ */
+ private AlignmentI alignment;
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected ProfilesI consensusProfiles;
+
+ /**
+ * HMM profile for the alignment
+ */
+ protected ProfilesI hmmProfiles;
+
+ /**
+ * results of cDNA complement consensus visible portion of view
*/
- protected AlignmentI alignment;
+ protected Hashtable[] hcomplementConsensus;
+
+ /**
+ * results of secondary structure base pair consensus for visible portion of
+ * view
+ */
+ protected Hashtable[] hStrucConsensus;
+
+ protected Conservation hconservation;
public AlignmentViewport(AlignmentI al)
{
return alignment.getGapCharacter();
}
- protected String sequenceSetID;
-
- /**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
- */
- protected boolean isDataset = false;
-
public void setDataset(boolean b)
{
isDataset = b;
return isDataset;
}
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
- protected ColumnSelection colSel = new ColumnSelection();
-
- public boolean autoCalculateConsensus = true;
-
- protected boolean autoCalculateStrucConsensus = true;
-
- protected boolean ignoreGapsInConsensusCalculation = false;
-
- protected ResidueShaderI residueShading = new ResidueShader();
-
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
{
return residueShading;
}
-
- protected AlignmentAnnotation consensus;
-
- protected AlignmentAnnotation complementConsensus;
-
- protected AlignmentAnnotation gapcounts;
-
- protected AlignmentAnnotation strucConsensus;
-
- protected AlignmentAnnotation conservation;
-
- protected AlignmentAnnotation quality;
-
- protected AlignmentAnnotation[] groupConsensus;
-
- protected AlignmentAnnotation[] groupConservation;
-
- /**
- * results of alignment consensus analysis for visible portion of view
- */
- protected ProfilesI hconsensus = null;
-
- /**
- * results of cDNA complement consensus visible portion of view
- */
- protected Hashtable[] hcomplementConsensus = null;
-
- /**
- * results of secondary structure base pair consensus for visible portion of
- * view
- */
- protected Hashtable[] hStrucConsensus = null;
-
- protected Conservation hconservation = null;
-
@Override
public void setConservation(Conservation cons)
{
}
@Override
- public void setSequenceConsensusHash(ProfilesI hconsensus)
+ public void setConsensusProfiles(ProfilesI hconsensus)
{
- this.hconsensus = hconsensus;
+ this.consensusProfiles = hconsensus;
}
@Override
}
@Override
- public ProfilesI getSequenceConsensusHash()
+ public ProfilesI getConsensusProfiles()
+ {
+ return consensusProfiles;
+ }
+
+ @Override
+ public void setHmmProfiles(ProfilesI info)
+ {
+ hmmProfiles = info;
+ }
+
+ @Override
+ public ProfilesI getHmmProfiles()
{
- return hconsensus;
+ return hmmProfiles;
}
@Override
}
@Override
- public AlignmentAnnotation getAlignmentGapAnnotation()
+ public AlignmentAnnotation getOccupancyAnnotation()
{
- return gapcounts;
+ return occupancy;
}
@Override
}
}
+ @Override
+ public void initInformationWorker(final AlignmentViewPanel ap)
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(InformationThread.class) == null)
+ {
+ calculator.registerWorker(new InformationThread(this, ap));
+ }
+ }
+
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
strucConsensus = null;
conservation = null;
quality = null;
- groupConsensus = null;
- groupConservation = null;
- hconsensus = null;
+ consensusProfiles = null;
hconservation = null;
hcomplementConsensus = null;
- gapcounts = null;
+ occupancy = null;
calculator = null;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
protected boolean showConsensusHistogram = true;
/**
+ * should hmm profile be rendered by default
+ */
+ protected boolean hmmShowSequenceLogo = false;
+
+ /**
+ * should hmm profile be rendered normalised to row height
+ */
+ protected boolean hmmNormaliseSequenceLogo = false;
+
+ /**
+ * should information histograms be rendered by default
+ */
+ protected boolean hmmShowHistogram = true;
+
+ /**
* @return the showConsensusProfile
*/
@Override
}
/**
+ * @return the showInformationProfile
+ */
+ @Override
+ public boolean isShowHMMSequenceLogo()
+ {
+ return hmmShowSequenceLogo;
+ }
+
+ /**
* @param showSequenceLogo
* the new value
*/
this.showSequenceLogo = showSequenceLogo;
}
+ public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+ {
+ if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
+ {
+ this.hmmShowSequenceLogo = showHMMSequenceLogo;
+ // TODO: updateAnnotation if description (tooltip) will show
+ // profile in place of information content?
+ // calculator.updateAnnotationFor(InformationThread.class);
+ }
+ this.hmmShowSequenceLogo = showHMMSequenceLogo;
+ }
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
}
/**
+ * @param showInformationHistogram
+ */
+ public void setShowInformationHistogram(boolean showInformationHistogram)
+ {
+ this.hmmShowHistogram = showInformationHistogram;
+ }
+
+ /**
* @return the showGroupConservation
*/
public boolean isShowGroupConservation()
}
/**
+ *
+ * @return flag to indicate if the information content histogram should be
+ * rendered by default
+ */
+ @Override
+ public boolean isShowInformationHistogram()
+ {
+ return this.hmmShowHistogram;
+ }
+
+ /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
ignoreGapsInConsensusCalculation = b;
if (ap != null)
{
- updateConsensus(ap);
if (residueShading != null)
{
residueShading.setThreshold(residueShading.getThreshold(),
ignoreGapsInConsensusCalculation);
}
}
+ }
+
+ public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+ {
+ ignoreBelowBackGroundFrequencyCalculation = b;
+ }
+ public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+ {
+ infoLetterHeight = b;
}
private long sgrouphash = -1, colselhash = -1;
return ignoreGapsInConsensusCalculation;
}
+ @Override
+ public boolean isIgnoreBelowBackground()
+ {
+ return ignoreBelowBackGroundFrequencyCalculation;
+ }
+
+ @Override
+ public boolean isInfoLetterHeight()
+ {
+ return infoLetterHeight;
+ }
+
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
if (alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = alignment.getHiddenColumns()
- .getVisibleSequenceStrings(start, end, seqs);
+ for (i = 0; i < iSize; i++)
+ {
+ Iterator<int[]> blocks = alignment.getHiddenColumns()
+ .getVisContigsIterator(start, end + 1, false);
+ selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+ }
}
else
{
{
if (start == 0)
{
- start = hidden.adjustForHiddenColumns(start);
+ start = hidden.visibleToAbsoluteColumn(start);
}
- end = hidden.getHiddenBoundaryRight(start);
+ end = hidden.getNextHiddenBoundary(false, start);
if (start == end)
{
end = max;
if (hidden != null && hidden.hasHiddenColumns())
{
- start = hidden.adjustForHiddenColumns(end);
- start = hidden.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.visibleToAbsoluteColumn(end);
+ start = hidden.getNextHiddenBoundary(true, start) + 1;
}
} while (end < max);
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- alignment.getHiddenColumns().makeVisibleAnnotation(
+ clone.makeVisibleAnnotation(
selectionGroup.getStartRes(), selectionGroup.getEndRes(),
- clone);
+ alignment.getHiddenColumns());
}
else
{
- alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+ clone.makeVisibleAnnotation(alignment.getHiddenColumns());
}
ala.add(clone);
}
{
alignment.padGaps();
}
- if (autoCalculateConsensus)
- {
- updateConsensus(ap);
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateStrucConsensus)
- {
- updateStrucConsensus(ap);
- }
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
updateAllColourSchemes();
calculator.restartWorkers();
- // alignment.adjustSequenceAnnotations();
}
/**
{
rs.alignmentChanged(alignment, hiddenRepSequences);
- rs.setConsensus(hconsensus);
+ rs.setConsensus(consensusProfiles);
if (rs.conservationApplied())
{
rs.setConservation(Conservation.calculateConservation("All",
// depending on if the user wants to see the annotation or not in a
// specific alignment
- if (hconsensus == null && !isDataset)
+ if (consensusProfiles == null && !isDataset)
{
if (!alignment.isNucleotide())
{
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- initGapCounts();
+
+ initOccupancy();
initComplementConsensus();
}
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts()
+ private void initOccupancy()
{
if (showOccupancy)
{
- gapcounts = new AlignmentAnnotation("Occupancy",
+ occupancy = new AlignmentAnnotation("Occupancy",
MessageManager.getString("label.occupancy_descr"),
new Annotation[1], 0f, alignment.getHeight(),
AlignmentAnnotation.BAR_GRAPH);
- gapcounts.hasText = true;
- gapcounts.autoCalculated = true;
- gapcounts.scaleColLabel = true;
- gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+ occupancy.hasText = true;
+ occupancy.autoCalculated = true;
+ occupancy.scaleColLabel = true;
+ occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
- alignment.addAnnotation(gapcounts);
+ alignment.addAnnotation(occupancy);
}
}
boolean showprf = isShowSequenceLogo();
boolean showConsHist = isShowConsensusHistogram();
boolean normLogo = isNormaliseSequenceLogo();
+ boolean showHMMPrf = isShowHMMSequenceLogo();
+ boolean showInfoHist = isShowInformationHistogram();
+ boolean normHMMLogo = isNormaliseHMMSequenceLogo();
/**
* TODO reorder the annotation rows according to group/sequence ordering on
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
sg.setNormaliseSequenceLogo(normLogo);
+ sg.setShowHMMSequenceLogo(showHMMPrf);
+ sg.setShowInformationHistogram(showInfoHist);
+ sg.setNormaliseHMMSequenceLogo(normHMMLogo);
}
if (conv)
{
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
- .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
return sq;
}
+ public boolean hasReferenceAnnotation()
+ {
+ AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
@Override
public void setCurrentTree(TreeModel tree)
{
{
return currentTree;
}
+
+ @Override
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return hmmNormaliseSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ hmmNormaliseSequenceLogo = state;
+ }
}
protected int alheight;
+ protected float widthRatio;
+
+ protected float heightRatio;
+
/**
* Create an OverviewDimensions object
*
public float getPixelsPerCol()
{
resetAlignmentDims();
- return (float) width / alwidth;
+ return 1 / widthRatio;
}
public float getPixelsPerSeq()
{
resetAlignmentDims();
- return (float) sequencesHeight / alheight;
+ return 1 / heightRatio;
}
public void setWidth(int w)
{
width = w;
+ widthRatio = (float) alwidth / width;
}
public void setHeight(int h)
{
sequencesHeight = h - graphHeight;
+ heightRatio = (float) alheight / sequencesHeight;
}
/**
// boxX, boxY is the x,y location equivalent to startRes, startSeq
int xPos = Math.min(startRes, alwidth - vpwidth + 1);
- boxX = Math.round((float) xPos * width / alwidth);
- boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+ boxX = Math.round(xPos / widthRatio);
+ boxY = Math.round(startSeq / heightRatio);
// boxWidth is the width in residues translated to pixels
- boxWidth = Math.round((float) vpwidth * width / alwidth);
+ boxWidth = Math.round(vpwidth / widthRatio);
// boxHeight is the height in sequences translated to pixels
- boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
+ boxHeight = Math.round(vpheight / heightRatio);
}
/**
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
public void adjustViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// calculate translation in pixel terms:
// get mouse location in viewport coords, add translation in viewport
// coords, and update viewport as usual
- int vpx = Math.round((float) mousex * alwidth / width);
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpx = Math.round(mousex * widthRatio);
+ int vpy = Math.round(mousey * heightRatio);
updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs,
hiddenCols);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh alwidth, alheight and width/height ratios
+ */
@Override
protected void updateViewportFromTopLeft(int leftx, int topy,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
int xAsRes = leftx;
int yAsSeq = topy;
- resetAlignmentDims();
if (xAsRes < 0)
{
public AlignmentColsCollectionI getColumns(AlignmentI al)
{
return new VisibleColsCollection(0,
- ranges.getAbsoluteAlignmentWidth() - 1, al);
+ ranges.getAbsoluteAlignmentWidth() - 1, al.getHiddenColumns());
}
@Override
{
alwidth = ranges.getVisibleAlignmentWidth();
alheight = ranges.getVisibleAlignmentHeight();
+
+ widthRatio = (float) alwidth / width;
+ heightRatio = (float) alheight / sequencesHeight;
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh widthRatio
+ */
@Override
protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
{
- int vpx = Math.round((float) mousex * alwidth / width);
+ int vpx = Math.round(mousex * widthRatio);
return vpx - ranges.getViewportWidth() / 2;
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh heightRatio
+ */
@Override
protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
{
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
return vpy - ranges.getViewportHeight() / 2;
}
public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// get alignment position of x and box (can get directly from vpranges) and
// calculate difference between the positions
- int vpx = Math.round((float) x * alwidth / width);
- int vpy = Math.round((float) y * alheight / sequencesHeight);
+ int vpx = Math.round(x * widthRatio);
+ int vpy = Math.round(y * heightRatio);
xdiff = ranges.getStartRes() - vpx;
ydiff = ranges.getStartSeq() - vpy;
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// convert mousex and mousey to alignment units as well as
// translating to top left corner of viewport - this is an absolute position
int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
// convert to visible positions
- int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+ int visXAsRes = hiddenCols.absoluteToVisibleColumn(xAsRes);
yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
public void adjustViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// calculate translation in pixel terms:
// get mouse location in viewport coords, add translation in viewport
// coords,
// convert back to pixel coords
int vpx = Math.round((float) mousex * alwidth / width);
- int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
+ int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff;
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
// update viewport accordingly
updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh alwidth, alheight and width/height ratios
+ */
@Override
protected void updateViewportFromTopLeft(int leftx, int topy,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
int visXAsRes = leftx;
int visYAsSeq = topy;
- resetAlignmentDims();
if (visXAsRes < 0)
{
int vpwidth = ranges.getViewportWidth();
// check in case we went off the edge of the alignment
- int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+ int visAlignWidth = hiddenCols.absoluteToVisibleColumn(alwidth - 1);
if (visXAsRes + vpwidth - 1 > visAlignWidth)
{
// went past the end of the alignment, adjust backwards
// if last position was before the end of the alignment, need to update
if (ranges.getEndRes() < visAlignWidth)
{
- visXAsRes = hiddenCols.findColumnPosition(hiddenCols
- .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+ visXAsRes = hiddenCols.absoluteToVisibleColumn(hiddenCols
+ .offsetByVisibleColumns(-(vpwidth - 1), alwidth - 1));
}
else
{
HiddenColumns hiddenCols)
{
// work with absolute values of startRes and endRes
- int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
- int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+ int startRes = hiddenCols.visibleToAbsoluteColumn(ranges.getStartRes());
+ int endRes = hiddenCols.visibleToAbsoluteColumn(ranges.getEndRes());
// work with absolute values of startSeq and endSeq
int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
{
alwidth = ranges.getAbsoluteAlignmentWidth();
alheight = ranges.getAbsoluteAlignmentHeight();
+
+ widthRatio = (float) alwidth / width;
+ heightRatio = (float) alheight / sequencesHeight;
}
+
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh widthRatio
+ */
@Override
protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
{
int vpx = Math.round((float) mousex * alwidth / width);
- return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+ return hidden.offsetByVisibleColumns(-ranges.getViewportWidth() / 2,
vpx);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh heightRatio
+ */
@Override
protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
{
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
}
public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// get alignment position of x and box (can get directly from vpranges) and
// calculate difference between the positions
- int vpx = Math.round((float) x * alwidth / width);
- int vpy = Math.round((float) y * alheight / sequencesHeight);
+ int vpx = Math.round(x * widthRatio);
+ int vpy = Math.round(y * heightRatio);
- xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
+ xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx);
ydiff = ranges.getStartSeq()
- hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
}
}
HiddenColumns hidden = al.getHiddenColumns();
- while (x < hidden.adjustForHiddenColumns(startRes))
+ while (x < hidden.visibleToAbsoluteColumn(startRes))
{
if (!scrollRight(false))
{
break;
}
}
- while (x > hidden.adjustForHiddenColumns(endRes))
+ while (x > hidden.visibleToAbsoluteColumn(endRes))
{
if (!scrollRight(true))
{
boolean changedLocation = false;
// convert the x,y location to visible coordinates
- int visX = al.getHiddenColumns().findColumnPosition(x);
+ int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
// if (vis_x,vis_y) is already visible don't do anything
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
updating = Collections.synchronizedMap(
new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
- canUpdate = new HashSet<AlignCalcWorkerI>();
+ canUpdate = new HashSet<>();
}
@Override
public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
Class<? extends AlignCalcWorkerI> workerClass)
{
- List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> workingClass = new ArrayList<>();
synchronized (canUpdate)
{
for (AlignCalcWorkerI worker : canUpdate)
public void removeRegisteredWorkersOfClass(
Class<? extends AlignCalcWorkerI> typeToRemove)
{
- List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
- Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> removable = new ArrayList<>();
+ Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
synchronized (restartable)
{
for (AlignCalcWorkerI worker : restartable)
* first just find those to remove (to avoid
* ConcurrentModificationException)
*/
- List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> toRemove = new ArrayList<>();
for (AlignCalcWorkerI worker : restartable)
{
if (worker.involves(ann))
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
{
AlignmentAnnotation consensus = getConsensusAnnotation();
consensus.annotations = new Annotation[aWidth];
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if (gap != null)
{
gap.annotations = new Annotation[aWidth];
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
- alignViewport.setSequenceConsensusHash(hconsensus);
+ alignViewport.setConsensusProfiles(hconsensus);
setColourSchemeConsensus(hconsensus);
}
*
* @return
*/
- protected AlignmentAnnotation getGapAnnotation()
+ protected AlignmentAnnotation getOccupancyAnnotation()
{
- return alignViewport.getAlignmentGapAnnotation();
+ return alignViewport.getOccupancyAnnotation();
}
/**
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
- AlignmentAnnotation gap = getGapAnnotation();
- if (gap != null)
+ AlignmentAnnotation occupancy = getOccupancyAnnotation();
+ if (occupancy != null)
{
- deriveGap(gap, hconsensus);
+ deriveOccupancy(occupancy, hconsensus);
}
}
}
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
ProfilesI hconsensus)
{
-
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
* @param hconsensus
* the computed consensus data
*/
- protected void deriveGap(AlignmentAnnotation gapAnnotation,
+ protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+ AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
- return alignViewport.getSequenceConsensusHash();
+ return alignViewport.getConsensusProfiles();
}
}
--- /dev/null
+package jalview.workers;
+
+import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This class calculates HMM Information Content annotations, based on any HMM
+ * consensus sequences and their HMM models. HMM consensus sequences may be
+ * present for the whole alignment, or subgroups of it.
+ *
+ */
+public class InformationThread extends AlignCalcWorker
+{
+ public static final String HMM_CALC_ID = "HMM";
+
+ /**
+ * Constructor
+ *
+ * @param alignViewport
+ * @param alignPanel
+ */
+ public InformationThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ /**
+ * Recomputes Information annotations for any HMM consensus sequences (for
+ * alignment and/or groups)
+ */
+ @Override
+ public void run()
+ {
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
+ calcMan.notifyStart(this);
+ // long started = System.currentTimeMillis();
+
+ try
+ {
+ if (calcMan.isPending(this))
+ {
+ // another instance of this is waiting to run
+ calcMan.workerComplete(this);
+ return;
+ }
+ while (!calcMan.notifyWorking(this))
+ {
+ // another thread in progress, wait my turn
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false, false);
+ }
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+
+ AlignmentI alignment = alignViewport.getAlignment();
+ int aWidth = alignment == null ? -1 : alignment.getWidth();
+ if (aWidth < 0)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ /*
+ * compute information profiles for any HMM consensus sequences
+ * for the alignment or sub-groups
+ */
+ computeProfiles(alignment);
+
+ /*
+ * construct the corresponding annotations
+ */
+ updateAnnotation();
+
+ if (ap != null)
+ {
+ ap.adjustAnnotationHeight();
+ ap.paintAlignment(true, true);
+ }
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.disableWorker(this);
+ ap.raiseOOMWarning("calculating information", error);
+ } finally
+ {
+ calcMan.workerComplete(this);
+ }
+ }
+
+ /**
+ * Computes HMM profiles for any HMM consensus sequences (for alignment or
+ * subgroups). Any alignment profile computed is stored on the viewport, any
+ * group profile computed is stored on the respective sequence group.
+ *
+ * @param alignment
+ * @see AlignViewportI#setHmmProfiles(ProfilesI)
+ */
+ protected void computeProfiles(AlignmentI alignment)
+ {
+ int width = alignment.getWidth();
+
+ /*
+ * alignment HMM profile
+ */
+ SequenceI seq = alignment.getHmmConsensus();
+ if (seq != null)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+ 0, width, alignViewport.isIgnoreBelowBackground(),
+ alignViewport.isInfoLetterHeight());
+ alignViewport.setHmmProfiles(hmmProfiles);
+ }
+
+ /*
+ * group HMM profiles
+ */
+ List<SequenceGroup> groups = alignment.getGroups();
+ for (SequenceGroup group : groups)
+ {
+ seq = group.getHmmConsensus();
+ if (seq != null)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+ 0, width, group.isIgnoreBelowBackground(),
+ group.isUseInfoLetterHeight());
+ group.setHmmProfiles(hmmProfiles);
+ }
+ }
+ }
+
+ /**
+ * gets the sequences on the alignment on the viewport.
+ *
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ /**
+ * Get the Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getOccupancyAnnotation();
+ }
+
+ /**
+ * Computes Information Content annotation for any HMM consensus sequences
+ * (for alignment or groups), and updates (or adds) the annotation to the
+ * sequence and the alignment
+ */
+ @Override
+ public void updateAnnotation()
+ {
+ AlignmentI alignment = alignViewport.getAlignment();
+
+ float maxInformation = 0f;
+ List<AlignmentAnnotation> infos = new ArrayList<>();
+
+ /*
+ * annotation for alignment HMM consensus if present
+ */
+ SequenceI hmmSeq = alignment.getHmmConsensus();
+ ProfilesI profile = alignViewport.getHmmProfiles();
+ float m = updateInformationAnnotation(hmmSeq, profile, null, infos);
+ maxInformation = Math.max(maxInformation, m);
+
+ /*
+ * annotation for group HMM consensus if present
+ */
+ for (SequenceGroup group : alignment.getGroups())
+ {
+ hmmSeq = group.getHmmConsensus();
+ ProfilesI profiles = group.getHmmProfiles();
+ m = updateInformationAnnotation(hmmSeq, profiles, group, infos);
+ maxInformation = Math.max(maxInformation, m);
+ }
+
+ /*
+ * maxInformation holds the maximum value of information score;
+ * set this as graphMax in all annotations to scale them all the same
+ */
+ for (AlignmentAnnotation ann : infos)
+ {
+ ann.graphMax = maxInformation;
+ }
+ }
+
+ /**
+ * Updates (and first constructs if necessary) an HMM Profile information
+ * content annotation for a sequence. The <code>group</code> argument is null
+ * for the whole alignment annotation, not null for a subgroup annotation. The
+ * updated annotation is added to the <code>infos</code> list. Answers the
+ * maximum information content value of any annotation (for use as a scaling
+ * factor for display).
+ *
+ * @param seq
+ * @param profile
+ * @param group
+ * @param infos
+ * @return
+ */
+ protected float updateInformationAnnotation(SequenceI seq,
+ ProfilesI profile, SequenceGroup group,
+ List<AlignmentAnnotation> infos)
+ {
+ if (seq == null || profile == null)
+ {
+ return 0f;
+ }
+
+ AlignmentAnnotation ann = findOrCreateAnnotation(seq, group);
+
+ seq.addAlignmentAnnotation(ann);
+ infos.add(ann);
+
+ float max = AAFrequency.completeInformation(ann, profile,
+ profile.getStartColumn(), profile.getEndColumn() + 1);
+
+ return max;
+ }
+
+ /**
+ * A helper method that first searches for the HMM annotation that matches the
+ * group reference (null for the whole alignment annotation). If found, its
+ * sequence reference is updated to the given sequence (the recomputed HMM
+ * consensus sequence). If not found, it is created. This supports both
+ * creating the annotation the first time hmmbuild is run, and updating it if
+ * hmmbuild is re-run.
+ *
+ * @param seq
+ * @param group
+ * @return
+ */
+ AlignmentAnnotation findOrCreateAnnotation(SequenceI seq,
+ SequenceGroup group)
+ {
+ /*
+ * can't use Alignment.findOrCreateAnnotation here because we
+ * want to update, rather than match on, the sequence ref
+ */
+ AlignmentAnnotation info = null;
+
+ AlignmentI alignment = alignViewport.getAlignment();
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
+ {
+ for (AlignmentAnnotation ann : anns)
+ {
+ if (HMM_CALC_ID.equals(ann.getCalcId()) && group == ann.groupRef)
+ {
+ info = ann;
+ info.setSequenceRef(seq);
+ info.label = seq.getName(); // in case group name changed!
+ break;
+ }
+ }
+ }
+
+ if (info == null)
+ {
+ int aWidth = alignment.getWidth();
+ String desc = MessageManager
+ .getString("label.information_description");
+ float graphMax = 6.52f; // todo where does this value derive from?
+ info = new AlignmentAnnotation(seq.getName(), desc,
+ new Annotation[aWidth], 0f, graphMax,
+ AlignmentAnnotation.BAR_GRAPH);
+ info.setCalcId(HMM_CALC_ID);
+ info.setSequenceRef(seq);
+ info.groupRef = group;
+ info.hasText = true;
+ alignment.addAnnotation(info);
+ }
+
+ return info;
+ }
+}
{
private static final String NEWLINE = System.lineSeparator();
+ public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
public interface FetchFinishedListenerI
{
void finished();
.getSequenceFetcherSingleton(progressIndicatorFrame);
// set default behaviour for transferring excess sequence data to the
// dataset
- trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+ trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
if (sources == null)
{
setDatabaseSources(featureSettings, isNucleotide);
*/
package jalview.ws.dbsources;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import com.stevesoft.pat.Regex;
*/
abstract public class Pfam extends Xfam
{
+ static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+
+ private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
public Pfam()
{
@Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
@Override
public Regex getAccessionValidator()
{
- // TODO Auto-generated method stub
return null;
}
@Override
public String getDbVersion()
{
- // TODO Auto-generated method stub
return null;
}
- /**
- * Returns base URL for selected Pfam alignment type
- *
- * @return PFAM URL stub for this DbSource
- */
@Override
- protected abstract String getXFAMURL();
+ protected String getURLPrefix()
+ {
+ return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+ }
/*
* (non-Javadoc)
super();
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.dbsources.Pfam#getPFAMURL()
- */
- @Override
- protected String getXFAMURL()
- {
- return "http://pfam.xfam.org/family/";
-
- }
-
@Override
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
return "/alignment/full";
}
super();
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.dbsources.Pfam#getPFAMURL()
- */
- @Override
- protected String getXFAMURL()
- {
- return "http://pfam.xfam.org/family/";
- }
-
@Override
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
return "/alignment/seed";
}
*/
package jalview.ws.dbsources;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import com.stevesoft.pat.Regex;
*/
abstract public class Rfam extends Xfam
{
+ static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
+
+ private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
+
+ @Override
+ protected String getURLPrefix()
+ {
+ return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
+ }
public Rfam()
{
@Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
@Override
public Regex getAccessionValidator()
{
- // TODO Auto-generated method stub
return null;
}
@Override
public String getDbVersion()
{
- // TODO Auto-generated method stub
return null;
}
- /**
- * Returns base URL for selected Rfam alignment type
- *
- * @return RFAM URL stub for this DbSource
- */
- @Override
- protected abstract String getXFAMURL();
-
/*
* (non-Javadoc)
*
super();
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.dbsources.Rfam#getXFAMURL()
- */
- @Override
- protected String getXFAMURL()
- {
- return "http://rfam.xfam.org/family/";
-
- }
-
@Override
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
return "/alignment/full";
}
super();
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.dbsources.Rfam#getRFAMURL()
- */
- @Override
- protected String getXFAMURL()
- {
- return "http://rfam.xfam.org/family/";
- }
-
@Override
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
// to download gzipped file add '?gzip=1'
return "/alignment/stockholm";
*/
package jalview.ws.dbsources;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
*/
public class Uniprot extends DbSourceProxyImpl
{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
private static final String BAR_DELIMITER = "|";
/*
super();
}
+ private String getDomain()
+ {
+ return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+ }
+
/*
* (non-Javadoc)
*
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- String downloadstring = "http://www.uniprot.org/uniprot/" + queries
+ String downloadstring = getDomain() + "/uniprot/" + queries
+ ".xml";
URL url = null;
URLConnection urlconn = null;
super();
}
- protected abstract String getXFAMURL();
+ /**
+ * the base URL for this Xfam-like service
+ *
+ * @return
+ */
+ protected abstract String getURLPrefix();
@Override
public abstract String getDbVersion();
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
- + getXFAMURLSUFFIX();
+ String xfamUrl = getURL(queries);
if (Cache.log != null)
{
return rcds;
}
+ String getURL(String queries)
+ {
+ return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+ + getURLSuffix();
+ }
+
/**
* Pfam and Rfam provide alignments
*/
*
* @return "" for most Xfam sources
*/
- public String getXFAMURLSUFFIX()
+ public String getURLSuffix()
{
return "";
}
{
// Adjust input view for gaps
// propagate insertions into profile
- alhidden = HiddenColumns.propagateInsertions(profileseq, al,
- input);
+ alhidden = al.propagateInsertions(profileseq, input);
}
}
}
/**
* input
*/
- ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+ ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
/**
* output
compbio.data.sequence.FastaSequence seq;
for (int i = 0, n = 0; i < seqs.length; i++)
{
-
String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
// for
// any
public List<Argument> getJabaArguments()
{
- List<Argument> newargs = new ArrayList<Argument>();
+ List<Argument> newargs = new ArrayList<>();
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
void displayResults(boolean newFrame)
{
// view input or result data for each block
- List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
+ List<AlignmentOrder> alorders = new ArrayList<>();
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
if (newFrame)
{
displayInNewFrame(al, alorders, hidden);
-
}
else
{
else
{
// construct a non-redundant ordering set
- List<String> names = new ArrayList<String>();
+ List<String> names = new ArrayList<>();
for (int i = 0, l = alorders.size(); i < l; i++)
{
String orderName = " Region " + i;
public enum ValueType
{
- Integer, Float, String
+ Integer, Float, String, Double
};
ValueType getType();
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ *
+ * @author TZVanaalten
+ *
+ */
+public class DoubleParameter extends Option implements ParameterI
+{
+ Double defval;
+
+ Double min, max;
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ return new ValueConstrainI()
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.Double;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ if (min < max)
+ {
+ return min;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public Number getMax()
+ {
+ if (min < max)
+ {
+ return max;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ };
+ }
+
+ public DoubleParameter(DoubleParameter parm)
+ {
+ super(parm);
+ max = parm.max;
+ min = parm.min;
+ }
+
+ public DoubleParameter(String name, String description, boolean required,
+ Double defValue, Double min, Double max)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ defval = defValue;
+ this.min = min;
+ this.max = max;
+ }
+
+ public DoubleParameter(String name, String description, boolean required,
+ Double defValue, Double value, Double min, Double max)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ defval = defValue;
+ this.min = min;
+ this.max = max;
+ }
+
+ @Override
+ public DoubleParameter copy()
+ {
+ return new DoubleParameter(this);
+ }
+}
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ *
+ * @author TZVanaalten
+ *
+ */
+public class LogarithmicParameter extends Option implements ParameterI
+{
+ Double defval;
+
+ Double min, max;
+
+ Double base;
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ return new ValueConstrainI()
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.Double;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ if (min < max)
+ {
+ return min;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public Number getMax()
+ {
+ if (min < max)
+ {
+ return max;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ };
+ }
+
+ public LogarithmicParameter(LogarithmicParameter parm)
+ {
+ super(parm);
+ max = parm.max;
+ min = parm.min;
+ base = parm.base;
+ }
+
+ public LogarithmicParameter(String name, String description,
+ boolean required, Double defValue, Double min, Double max,
+ Double base)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ defval = defValue;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
+ this.base = base;
+ }
+
+ public LogarithmicParameter(String name, String description,
+ boolean required, Double defValue, Double value, Double min,
+ Double max, Double base)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ defval = defValue;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
+ this.base = base;
+ }
+
+ @Override
+ public LogarithmicParameter copy()
+ {
+ return new LogarithmicParameter(this);
+ }
+
+ public Double getBase()
+ {
+ return base;
+ }
+}
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+import java.net.URL;
+import java.util.List;
+
+public class StringParameter extends Option implements ParameterI
+{
+
+ @Override
+ public URL getFurtherDetails()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isRequired()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ // TODO Auto-generated method stub
+ return description;
+ }
+
+ @Override
+ public List<String> getPossibleValues()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getName()
+ {
+ // TODO Auto-generated method stub
+ return name;
+ }
+
+ @Override
+ public String getValue()
+ {
+ // TODO Auto-generated method stub
+ return value;
+ }
+
+ @Override
+ public void setValue(String selectedItem)
+ {
+ value = selectedItem;
+
+ }
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ // TODO Auto-generated method stub
+ return new StringValueConstrain();
+ }
+
+ @Override
+ public ParameterI copy()
+ {
+ return new StringParameter(this);
+ }
+
+ private class StringValueConstrain implements ValueConstrainI
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.String;
+ }
+
+ @Override
+ public Number getMax()
+ {
+ return null;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ return null;
+ }
+
+ }
+
+ public StringParameter(StringParameter parm)
+ {
+ this.name = parm.name;
+ this.defvalue = parm.defvalue;
+ }
+
+ public StringParameter(String name, String description, boolean required,
+ String defValue)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ this.defvalue = defValue;
+ }
+
+ public StringParameter(String name, String description, boolean required,
+ String defValue, String value)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ this.defvalue = defValue;
+ }
+}
private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
+ /**
+ * PDB sequence position to sequence coordinate mapping as derived from SIFTS
+ * record for the identified SeqCoordSys Used for lift-over from sequence
+ * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence
+ * being annotated with PDB data
+ */
+ private jalview.datamodel.Mapping seqFromPdbMapping;
+
private static final int BUFFER_SIZE = 4096;
- public static final int UNASSIGNED = -1;
+ public static final int UNASSIGNED = Integer.MIN_VALUE;
private static final int PDB_RES_POS = 0;
private static final int PDB_ATOM_POS = 1;
+ private static final int PDBE_POS = 2;
+
private static final String NOT_OBSERVED = "Not_Observed";
private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
public StructureMapping getSiftsStructureMapping(SequenceI seq,
String pdbFile, String chain) throws SiftsException
{
+ SequenceI aseq = seq;
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ seq.getName());
HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
String mappingOutput = mappingDetails.toString();
- StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
- pdbId, chain, mapping, mappingOutput);
+ StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile,
+ pdbId, chain, mapping, mappingOutput, seqFromPdbMapping);
+
return siftsMapping;
}
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
- List<Integer> omitNonObserved = new ArrayList<Integer>();
- int nonObservedShiftIndex = 0;
+ List<Integer> omitNonObserved = new ArrayList<>();
+ int nonObservedShiftIndex = 0,pdbeNonObserved=0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
- omitNonObserved, nonObservedShiftIndex);
+ omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
processSegments(segments, shp);
try
{
{
throw new SiftsException("SIFTS mapping failed");
}
+ // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
Integer[] keys = mapping.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
-
+ List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
+ int[]_cfrom=null,_cto=null;
String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED)
+ if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
{
+ for (int seqps:keys)
+ {
+ int pdbpos = mapping.get(seqps)[PDBE_POS];
+ if (pdbpos == UNASSIGNED)
+ {
+ // not correct - pdbpos might be -1, but leave it for now
+ continue;
+ }
+ if (_cfrom==null || seqps!=_cfrom[1]+1)
+ {
+ _cfrom = new int[] { seqps,seqps};
+ from.add(_cfrom);
+ _cto = null; // discontinuity
+ } else {
+ _cfrom[1]= seqps;
+ }
+ if (_cto==null || pdbpos!=1+_cto[1])
+ {
+ _cto = new int[] { pdbpos,pdbpos};
+ to.add(_cto);
+ } else {
+ _cto[1] = pdbpos;
+ }
+ }
+ _cfrom = new int[from.size() * 2];
+ _cto = new int[to.size() * 2];
+ int p = 0;
+ for (int[] range : from)
+ {
+ _cfrom[p++] = range[0];
+ _cfrom[p++] = range[1];
+ }
+ ;
+ p = 0;
+ for (int[] range : to)
+ {
+ _cto[p++] = range[0];
+ _cto[p++] = range[1];
+ }
+ ;
+
+ seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
+ 1,
+ 1);
pdbStart = mapping.get(seqStart)[PDB_RES_POS];
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
int orignalSeqStart = seq.getStart();
TreeMap<Integer, String> resNumMap = shp.getResNumMap();
List<Integer> omitNonObserved = shp.getOmitNonObserved();
int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
+ int pdbeNonObservedCount = shp.getPdbeNonObserved();
+ int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
// System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
+ boolean isObserved = isResidueObserved(residue);
+ int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+ UNASSIGNED);
int currSeqIndex = UNASSIGNED;
List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
CrossRefDb pdbRefDb = null;
if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
{
pdbRefDb = cRefDb;
+ if (firstPDBResNum == UNASSIGNED)
+ {
+ firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ UNASSIGNED);
+ }
+ else
+ {
+ if (isObserved)
+ {
+ // after we find the first observed residue we just increment
+ firstPDBResNum++;
+ }
+ }
}
if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
}
}
}
+ if (!isObserved)
+ {
+ ++pdbeNonObservedCount;
+ }
+ if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
+ // ???
+ {
+ // if the sequence has a primary reference to the PDB, then we are
+ // dealing with a sequence extracted directly from the PDB. In that
+ // case, numbering is PDBe - non-observed residues
+ currSeqIndex = seq.getStart() - 1 + pdbeIndex;
+ }
+ if (!isObserved)
+ {
+ if (seqCoordSys != CoordinateSys.UNIPROT) // FIXME: PDB or PDBe only
+ // here
+ {
+ // mapping to PDB or PDBe so we need to bookkeep for the
+ // non-observed
+ // SEQRES positions
+ omitNonObserved.add(currSeqIndex);
+ ++nonObservedShiftIndex;
+ }
+ }
if (currSeqIndex == UNASSIGNED)
{
+ // change in logic - unobserved residues with no currSeqIndex
+ // corresponding are still counted in both nonObservedShiftIndex and
+ // pdbeIndex...
continue;
}
- if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
+ // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
+ // true
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
int resNum = (pdbRefDb == null)
: getLeadingIntegerValue(pdbRefDb.getDbResNum(),
UNASSIGNED);
- if (isResidueObserved(residue)
- || seqCoordSys == CoordinateSys.UNIPROT)
+ if (isObserved)
{
char resCharCode = ResidueProperties
.getSingleCharacterCode(ResidueProperties
.getCanonicalAminoAcid(residue.getDbResName()));
resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+
+ int[] mappingcols = new int[] { Integer.valueOf(resNum),
+ UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED };
+
+ mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols);
}
- else
- {
- omitNonObserved.add(currSeqIndex);
- ++nonObservedShiftIndex;
- }
- mapping.put(currSeqIndex - nonObservedShiftIndex,
- new int[]
- { Integer.valueOf(resNum), UNASSIGNED });
}
}
}
private int nonObservedShiftIndex;
+ /**
+ * count of number of 'not observed' positions in the PDB record's SEQRES
+ * (total number of residues with coordinates == length(SEQRES) -
+ * pdbeNonObserved
+ */
+ private int pdbeNonObserved;
+
public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
TreeMap<Integer, String> resNumMap,
- List<Integer> omitNonObserved, int nonObservedShiftIndex)
+ List<Integer> omitNonObserved, int nonObservedShiftIndex,
+ int pdbeNonObserved)
{
setSeq(seq);
setMapping(mapping);
setResNumMap(resNumMap);
setOmitNonObserved(omitNonObserved);
setNonObservedShiftIndex(nonObservedShiftIndex);
+ setPdbeNonObserved(pdbeNonObserved);
+
}
+ public void setPdbeNonObserved(int pdbeNonObserved2)
+ {
+ this.pdbeNonObserved = pdbeNonObserved2;
+ }
+
+ public int getPdbeNonObserved()
+ {
+ return pdbeNonObserved;
+ }
public SequenceI getSeq()
{
return seq;
{
this.nonObservedShiftIndex = nonObservedShiftIndex;
}
+
}
@Override
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AAFrequencyTest
{
+ HiddenMarkovModel hmm;
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws IOException, MalformedURLException
+ {
+ /*
+ * load a dna (ACGT) HMM file to a HiddenMarkovModel
+ */
+ HMMFile hmmFile = new HMMFile(new FileParse(
+ "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
+ hmm = hmmFile.getHMM();
+ }
+
@Test(groups = { "Functional" })
public void testCalculate_noProfile()
{
assertEquals("T 75%", ann.description);
assertEquals("T", ann.displayCharacter);
}
+
+ @Test(groups = { "Functional" })
+ public void testExtractHMMProfile()
+ throws MalformedURLException, IOException
+ {
+ int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
+ int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false, false);
+ for (int i = 0; i < actual.length; i++)
+ {
+ if (i == 2)
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ else
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ }
+
+ int[] expected2 = { 0, 4, 100, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
+ int[] actual2 = AAFrequency.extractHMMProfile(hmm, 2, true, false);
+ for (int i = 0; i < actual2.length; i++)
+ {
+ if (i == 2)
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ else
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ }
+
+ assertNull(AAFrequency.extractHMMProfile(null, 98978867, true, false));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetAnalogueCount()
+ {
+ /*
+ * 'T' in column 0 has emission probability 0.7859, scales to 7859
+ */
+ int count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, false);
+ assertEquals(7859, count);
+
+ /*
+ * same with 'use info height': value is multiplied by log ratio
+ * log(value / background) / log(2) = log(0.7859/0.25)/0.693
+ * = log(3.1)/0.693 = 1.145/0.693 = 1.66
+ * so value becomes 1.2987 and scales up to 12987
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, true);
+ assertEquals(12987, count);
+
+ /*
+ * 'G' in column 20 has emission probability 0.75457, scales to 7546
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false, false);
+ assertEquals(7546, count);
+
+ /*
+ * 'G' in column 1077 has emission probability 0.0533, here
+ * ignored (set to 0) since below background of 0.25
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true, false);
+ assertEquals(0, count);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCompleteInformation()
+ {
+ ProfileI prof1 = new Profile(1, 0, 100, "A");
+ ProfileI prof2 = new Profile(1, 0, 100, "-");
+
+ ProfilesI profs = new Profiles(new ProfileI[] { prof1, prof2 });
+ Annotation ann1 = new Annotation(6.5f);
+ Annotation ann2 = new Annotation(0f);
+ Annotation[] annots = new Annotation[] { ann1, ann2 };
+ SequenceI seq = new Sequence("", "AA", 0, 0);
+ seq.setHMM(hmm);
+ AlignmentAnnotation annot = new AlignmentAnnotation("", "", annots);
+ annot.setSequenceRef(seq);
+ AAFrequency.completeInformation(annot, profs, 0, 1);
+ float ic = annot.annotations[0].value;
+ assertEquals(0.91532f, ic, 0.0001f);
+ ic = annot.annotations[1].value;
+ assertEquals(0f, ic, 0.0001f);
+ int i = 0;
+ }
+
}
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
List<DnaVariant> codon1Variants = new ArrayList<>();
List<DnaVariant> codon2Variants = new ArrayList<>();
List<DnaVariant> codon3Variants = new ArrayList<>();
+
List<DnaVariant> codonVariants[] = new ArrayList[3];
codonVariants[0] = codon1Variants;
codonVariants[1] = codon2Variants;
* Case 2: CDS 3 times length of peptide + stop codon
* (note code does not currently check trailing codon is a stop codon)
*/
- dna = new Sequence("dna", "AACGacgtCTCCTTGA");
+ dna = new Sequence("dna", "AACGacgtCTCCTCCC");
dna.createDatasetSequence();
dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
Arrays.deepToString(ml.getFromRanges().toArray()));
/*
- * Case 3: CDS not 3 times length of peptide - no mapping is made
+ * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 4: CDS shorter than 3 * peptide - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCC");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
*/
dna = new Sequence("dna", "AACGacgtCTCCTTG");
dna.createDatasetSequence();
dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
- assertNull(ml);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
/*
- * Case 4: incomplete start codon corresponding to X in peptide
+ * Case 6: incomplete start codon corresponding to X in peptide
*/
dna = new Sequence("dna", "ACGacgtCTCCTTGG");
dna.createDatasetSequence();
assertEquals("[[3, 3], [8, 12]]",
Arrays.deepToString(ml.getFromRanges().toArray()));
}
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ */
+ @Test
+ public void testFindCdsForProtein()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(
+ new int[]
+ { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - no dna-to-CDS mapping exists - search fails
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * second case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * third case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
+ }
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ * This test is for the case where transcript and CDS are the same length.
+ */
+ @Test
+ public void testFindCdsForProtein_noUTR()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(
+ new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - transcript lacks CDS features - it appears to be
+ * the CDS sequence and is returned
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertSame(seq, dna1.getDatasetSequence());
+
+ /*
+ * second case - transcript has CDS feature - this means it is
+ * not returned as a match for CDS (CDS sequences don't have CDS features)
+ */
+ dna1.addSequenceFeature(
+ new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * third case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * fourth case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
+ }
}
public void testFindXrefSourcesForSequence_proteinToDna()
{
SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
- List<String> sources = new ArrayList<String>();
+ List<String> sources = new ArrayList<>();
AlignmentI al = new Alignment(new SequenceI[] {});
/*
sources = new CrossRef(new SequenceI[] { seq }, al)
.findXrefSourcesForSequences(false);
// method is patched to remove EMBL from the sources to match
- assertEquals(3, sources.size());
- assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+ assertEquals(4, sources.size());
+ assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
+ sources.toString());
/*
* add a sequence to the alignment which has a dbref to UNIPROT|A1234
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
- List<SequenceI> result = new ArrayList<SequenceI>();
+ List<SequenceI> result = new ArrayList<>();
/*
* first search for a dbref nowhere on the alignment:
import jalview.io.FormatAdapter;
import java.io.IOException;
+import java.util.Iterator;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
assertNotNull("Couldn't do a full width translation of test data.",
translated);
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
- int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
+ Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
+ alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
AlignmentI transAlf = dna.translateCdna();
DataSourceType.PASTE, FileFormat.Fasta);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
AlignViewportI av = new AlignViewport(alf, cs);
- Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
.generate(12, 8, 97, 5, 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
- Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+ false);
+ Dna dna = new Dna(av, contigs);
AlignmentI translated = dna.translateCdna();
/*
}
AlignmentI cdnaReordered = new Alignment(sorted);
av = new AlignViewport(cdnaReordered, cs);
- dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+ contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+ dna = new Dna(av, contigs);
AlignmentI translated2 = dna.translateCdna();
/*
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
- Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+ Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+ false);
+ Dna testee = new Dna(av, contigs);
AlignmentI reversed = testee.reverseCdna(false);
assertEquals(1, reversed.getHeight());
assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
public void testFindDistances_withParams()
{
AlignFrame af = setupAlignmentView();
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
AlignmentView view = viewport.getAlignmentView(false);
ScoreModelI sm = new FeatureDistanceModel();
*/
package jalview.datamodel;
+import static org.testng.Assert.assertNull;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
import jalview.analysis.AlignSeq;
import jalview.gui.JvOptionPane;
Assert.assertTrue(ann.isQuantitative(),
"Mixed 'E' annotation set should be quantitative.");
}
+
+ @Test(groups = "Functional")
+ public void testMakeVisibleAnnotation()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
+ anns);
+
+ // null annotations
+ AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann",
+ null);
+ emptyann.makeVisibleAnnotation(h);
+ assertNull(emptyann.annotations);
+
+ emptyann.makeVisibleAnnotation(3, 4, h);
+ assertNull(emptyann.annotations);
+
+ // without bounds, does everything
+ ann.makeVisibleAnnotation(h);
+ assertEquals(12, ann.annotations.length);
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[1]);
+ assertEquals(1.0f, ann.annotations[2].value);
+ assertEquals(2.0f, ann.annotations[3].value);
+ assertEquals(3.0f, ann.annotations[4].value);
+ assertNull(ann.annotations[5]);
+ assertNull(ann.annotations[6]);
+ assertEquals(4.0f, ann.annotations[7].value);
+ assertEquals(5.0f, ann.annotations[8].value);
+ assertEquals(6.0f, ann.annotations[9].value);
+ assertEquals(7.0f, ann.annotations[10].value);
+ assertEquals(8.0f, ann.annotations[11].value);
+
+ // without hidden cols, just truncates
+ ann.makeVisibleAnnotation(3, 5, h);
+ assertEquals(3, ann.annotations.length);
+ assertEquals(2.0f, ann.annotations[0].value);
+ assertEquals(3.0f, ann.annotations[1].value);
+ assertNull(ann.annotations[2]);
+
+ anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h.hideColumns(4, 7);
+ ann.makeVisibleAnnotation(1, 9, h);
+ assertEquals(5, ann.annotations.length);
+ assertNull(ann.annotations[0]);
+ assertEquals(1.0f, ann.annotations[1].value);
+ assertEquals(2.0f, ann.annotations[2].value);
+ assertEquals(5.0f, ann.annotations[3].value);
+ assertEquals(6.0f, ann.annotations[4].value);
+
+ anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h.hideColumns(1, 2);
+ ann.makeVisibleAnnotation(1, 9, h);
+ assertEquals(3, ann.annotations.length);
+ assertEquals(2.0f, ann.annotations[0].value);
+ assertEquals(5.0f, ann.annotations[1].value);
+ assertEquals(6.0f, ann.annotations[2].value);
+
+ anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8), new Annotation(9), new Annotation(10),
+ new Annotation(11), new Annotation(12), new Annotation(13),
+ new Annotation(14), new Annotation(15) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h = new HiddenColumns();
+ h.hideColumns(5, 18);
+ h.hideColumns(20, 21);
+ ann.makeVisibleAnnotation(1, 21, h);
+ assertEquals(5, ann.annotations.length);
+ assertEquals(1.0f, ann.annotations[1].value);
+ assertEquals(2.0f, ann.annotations[2].value);
+ assertEquals(3.0f, ann.annotations[3].value);
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[4]);
+ }
}
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
import jalview.util.MapList;
import java.io.IOException;
if (raiseAssert)
{
Assert.fail(message
- + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+ + " DBRefEntry " + dbr + " for sequence "
+ + seqds
+ + " in alignment has map to sequence not in dataset");
}
return false;
}
// third found.. so
assertFalse(iter.hasNext());
+ // search for annotation on one sequence with a particular label - expect
+ // one
+ SequenceI sqfound;
+ anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+ "Secondary Structure");
+ iter = anns.iterator();
+ assertTrue(iter.hasNext());
+ // expect reference to sequence 1 in the alignment
+ assertTrue(sqfound == iter.next().sequenceRef);
+ assertFalse(iter.hasNext());
+
// null on all parameters == find all annotations
anns = al.findAnnotations(null, null, null);
iter = anns.iterator();
// todo test coverage for annotations, mappings, groups,
// hidden sequences, properties
}
+
+ /**
+ * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+ * an annotation with a null calcId
+ *
+ */
+ @Test(groups = "Functional")
+ public void testFindOrCreateForNullCalcId()
+ {
+ SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+ AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+ "Temperature Factor", null, false, seq, null);
+ assertNotNull(ala);
+ assertEquals(seq, ala.sequenceRef);
+ assertEquals("", ala.getCalcId());
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertions()
+ {
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // force different kinds of padding
+ al.getSequenceAt(3).deleteChars(2, 23);
+ al.getSequenceAt(4).deleteChars(2, 27);
+ al.getSequenceAt(5).deleteChars(10, 27);
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(15, 17);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+ int[] region = visible.next();
+ assertEquals("[0, 14]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[18, 24]", Arrays.toString(region));
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 25, false);
+ region = visible.next();
+ assertEquals("[0, 10]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[14, 24]", Arrays.toString(region));
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertionsOverlap()
+ {
+ // test propagateInsertions where gaps and hiddenColumns overlap
+
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+
+ // hide columns so that some overlap with the gaps
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(7, 10);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+ int[] region = visible.next();
+ assertEquals("[0, 6]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[11, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 20, false);
+ region = visible.next();
+ assertEquals("[0, 4]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPadGaps()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ a.setGapCharacter('.'); // this replaces existing gaps
+ assertEquals("ABCDEF..", seq1.getSequenceAsString());
+ a.padGaps();
+ // trailing gaps are pruned, short sequences padded with gap character
+ assertEquals("ABCDEF.", seq1.getSequenceAsString());
+ assertEquals(".JKLMNO", seq2.getSequenceAsString());
+ assertEquals(".PQR...", seq3.getSequenceAsString());
+ }
}
import static org.testng.Assert.assertEquals;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
">s1\n0123456789\n", DataSourceType.PASTE);
- AlignViewport av = af.getViewport();
+ AlignmentViewport av = af.getViewport();
AlignmentView view = av.getAlignmentView(true);
/*
import java.util.BitSet;
import java.util.Collections;
import java.util.ConcurrentModificationException;
+import java.util.Iterator;
import java.util.List;
import org.testng.annotations.BeforeClass;
// hide column 5 (and adjacent):
cs.hideSelectedColumns(5, al.getHiddenColumns());
// 4,5,6 now hidden:
- List<int[]> hidden = al.getHiddenColumns().getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ Iterator<int[]> regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
// none now selected:
assertTrue(cs.getSelected().isEmpty());
cs.addElement(5);
cs.addElement(6);
cs.hideSelectedColumns(4, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
assertTrue(cs.getSelected().isEmpty());
// repeat, hiding column (4, 5 and) 6
cs.addElement(5);
cs.addElement(6);
cs.hideSelectedColumns(6, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
assertTrue(cs.getSelected().isEmpty());
// repeat, with _only_ adjacent columns selected
cs.addElement(4);
cs.addElement(6);
cs.hideSelectedColumns(5, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
assertTrue(cs.getSelected().isEmpty());
}
cs.hideSelectedColumns(al);
assertTrue(cs.getSelected().isEmpty());
- List<int[]> hidden = cols.getHiddenColumnsCopy();
- assertEquals(4, hidden.size());
- assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
- assertEquals("[7, 9]", Arrays.toString(hidden.get(1)));
- assertEquals("[15, 18]", Arrays.toString(hidden.get(2)));
- assertEquals("[20, 22]", Arrays.toString(hidden.get(3)));
+ Iterator<int[]> regions = cols.iterator();
+ assertEquals(4, cols.getNumberOfRegions());
+ assertEquals("[2, 4]", Arrays.toString(regions.next()));
+ assertEquals("[7, 9]", Arrays.toString(regions.next()));
+ assertEquals("[15, 18]", Arrays.toString(regions.next()));
+ assertEquals("[20, 22]", Arrays.toString(regions.next()));
}
/**
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMNodeTest
+{
+ private HiddenMarkovModel hmm;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws MalformedURLException, IOException
+ {
+ /*
+ * load hmm model of a Kinase domain to a HiddenMarkovModel
+ */
+ HMMFile file = new HMMFile(new FileParse(
+ "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+ hmm = file.getHMM();
+ }
+
+ @Test(groups="Functional")
+ public void testGetMaxMatchEmissionIdex()
+ {
+ assertEquals(hmm.getAlphabetType(), "amino");
+ String symbols = hmm.getSymbols();
+
+ assertEquals(hmm.getNode(1).getMaxMatchEmissionIndex(),
+ symbols.indexOf('Y'));
+
+ assertEquals(hmm.getNode(17).getMaxMatchEmissionIndex(),
+ symbols.indexOf('K'));
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class HiddenColumnsCursorTest
+{
+
+ @Test(groups = { "Functional" })
+ public void testConstructor()
+ {
+ HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+ assertNull(cursor.findRegionForColumn(0, false));
+
+ List<int[]> hlist = new ArrayList<>();
+ cursor = new HiddenColumnsCursor(hlist);
+ assertNull(cursor.findRegionForColumn(0, false));
+
+ cursor = new HiddenColumnsCursor(hlist, 3, 12);
+ assertNull(cursor.findRegionForColumn(0, false));
+
+ hlist.add(new int[] { 3, 7 });
+ hlist.add(new int[] { 15, 25 });
+ cursor = new HiddenColumnsCursor(hlist);
+ HiddenCursorPosition p = cursor.findRegionForColumn(8, false);
+ assertEquals(1, p.getRegionIndex());
+
+ cursor = new HiddenColumnsCursor(hlist, 1, 5);
+ p = cursor.findRegionForColumn(8, false);
+ assertEquals(1, p.getRegionIndex());
+ }
+
+ /**
+ * Test the method which finds the corresponding region given a column
+ */
+ @Test(groups = { "Functional" })
+ public void testFindRegionForColumn()
+ {
+ HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+ HiddenCursorPosition pos = cursor.findRegionForColumn(20, false);
+ assertNull(pos);
+
+ List<int[]> hidden = new ArrayList<>();
+ hidden.add(new int[] { 53, 76 });
+ hidden.add(new int[] { 104, 125 });
+
+ cursor = new HiddenColumnsCursor(hidden);
+
+ int regionIndex = cursor.findRegionForColumn(126, false).getRegionIndex();
+ assertEquals(2, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(125, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(108, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(104, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(103, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(77, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(76, false).getRegionIndex();
+ assertEquals(0, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(53, false).getRegionIndex();
+ assertEquals(0, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(52, false).getRegionIndex();
+ assertEquals(0, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(0, false).getRegionIndex();
+ assertEquals(0, regionIndex);
+
+ hidden.add(new int[] { 138, 155 });
+
+ cursor = new HiddenColumnsCursor(hidden);
+
+ regionIndex = cursor.findRegionForColumn(160, false).getRegionIndex();
+ assertEquals(3, regionIndex);
+
+ regionIndex = cursor.findRegionForColumn(100, false).getRegionIndex();
+ assertEquals(1, regionIndex);
+ }
+
+ /**
+ * Test the method which counts the number of hidden columns before a column
+ */
+ @Test(groups = { "Functional" })
+ public void testFindRegionForColumn_Visible()
+ {
+ HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+ HiddenCursorPosition pos = cursor.findRegionForColumn(20, true);
+ assertNull(pos);
+
+ List<int[]> hidden = new ArrayList<>();
+ hidden.add(new int[] { 53, 76 });
+ hidden.add(new int[] { 104, 125 });
+
+ cursor = new HiddenColumnsCursor(hidden);
+
+ int offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
+ assertEquals(46, offset);
+
+ offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
+ assertEquals(24, offset);
+
+ offset = cursor.findRegionForColumn(53, true).getHiddenSoFar();
+ assertEquals(24, offset);
+
+ offset = cursor.findRegionForColumn(52, true).getHiddenSoFar();
+ assertEquals(0, offset);
+
+ offset = cursor.findRegionForColumn(10, true).getHiddenSoFar();
+ assertEquals(0, offset);
+
+ offset = cursor.findRegionForColumn(0, true).getHiddenSoFar();
+ assertEquals(0, offset);
+
+ offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
+ assertEquals(24, offset);
+
+ offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
+ assertEquals(46, offset);
+ }
+}
import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignmentGenerator;
-import jalview.gui.JvOptionPane;
import java.util.Arrays;
import java.util.BitSet;
-import java.util.List;
-import java.util.Random;
+import java.util.Iterator;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class HiddenColumnsTest
{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
/**
* Test the method which counts the number of hidden columns
*/
public void testFindColumnPosition()
{
HiddenColumns cs = new HiddenColumns();
- assertEquals(5, cs.findColumnPosition(5));
+ assertEquals(5, cs.absoluteToVisibleColumn(5));
// hiding column 6 makes no difference
cs.hideColumns(6, 6);
- assertEquals(5, cs.findColumnPosition(5));
+ assertEquals(5, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 5 to column 4
cs.hideColumns(4, 4);
- assertEquals(4, cs.findColumnPosition(5));
+ assertEquals(4, cs.absoluteToVisibleColumn(5));
// hiding column 4 moves column 4 to position 3
- assertEquals(3, cs.findColumnPosition(4));
+ assertEquals(3, cs.absoluteToVisibleColumn(4));
// hiding columns 1 and 2 moves column 5 to column 2
cs.hideColumns(1, 2);
- assertEquals(2, cs.findColumnPosition(5));
+ assertEquals(2, cs.absoluteToVisibleColumn(5));
// check with > 1 hidden column regions
// where some columns are in the hidden regions
cs2.hideColumns(40, 44);
// hiding columns 5-10 and 20-27 moves column 8 to column 4
- assertEquals(4, cs2.findColumnPosition(8));
+ assertEquals(4, cs2.absoluteToVisibleColumn(8));
// and moves column 24 to 13
- assertEquals(13, cs2.findColumnPosition(24));
+ assertEquals(13, cs2.absoluteToVisibleColumn(24));
// and moves column 28 to 14
- assertEquals(14, cs2.findColumnPosition(28));
+ assertEquals(14, cs2.absoluteToVisibleColumn(28));
// and moves column 40 to 25
- assertEquals(25, cs2.findColumnPosition(40));
+ assertEquals(25, cs2.absoluteToVisibleColumn(40));
// check when hidden columns start at 0 that the visible column
// is returned as 0
HiddenColumns cs3 = new HiddenColumns();
cs3.hideColumns(0, 4);
- assertEquals(0, cs3.findColumnPosition(2));
+ assertEquals(0, cs3.absoluteToVisibleColumn(2));
+ // check that column after the last hidden region doesn't crash
+ assertEquals(46, cs2.absoluteToVisibleColumn(65));
}
- /**
- * Test the method that finds the visible column position a given distance
- * before another column
- */
@Test(groups = { "Functional" })
- public void testFindColumnNToLeft()
+ public void testVisibleContigsIterator()
{
HiddenColumns cs = new HiddenColumns();
- // test that without hidden columns, findColumnNToLeft returns
- // position n to left of provided position
- int pos = cs.subtractVisibleColumns(3, 10);
- assertEquals(7, pos);
-
- // 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
- assertEquals(10, pos);
-
- // overflow to left returns negative number
- pos = cs.subtractVisibleColumns(3, 0);
- assertEquals(-3, pos);
-
- // test that with hidden columns to left of result column
- // behaviour is the same as above
- cs.hideColumns(1, 3);
-
- // position n to left of provided position
- pos = cs.subtractVisibleColumns(3, 10);
- assertEquals(7, pos);
-
- // 0 returns same position
- pos = cs.subtractVisibleColumns(0, 10);
- assertEquals(10, pos);
-
- // test with one set of hidden columns between start and required position
- cs.hideColumns(12, 15);
- pos = cs.subtractVisibleColumns(8, 17);
- assertEquals(5, pos);
-
- // test with two sets of hidden columns between start and required position
- cs.hideColumns(20, 21);
- pos = cs.subtractVisibleColumns(8, 23);
- assertEquals(9, pos);
-
- // repeat last 2 tests with no hidden columns to left of required position
- ColumnSelection colsel = new ColumnSelection();
- cs.revealAllHiddenColumns(colsel);
-
- // test with one set of hidden columns between start and required position
- cs.hideColumns(12, 15);
- pos = cs.subtractVisibleColumns(8, 17);
- assertEquals(5, pos);
-
- // test with two sets of hidden columns between start and required position
- cs.hideColumns(20, 21);
- pos = cs.subtractVisibleColumns(8, 23);
- assertEquals(9, pos);
-
- }
+ Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
+ int[] region = visible.next();
+ assertEquals("[3, 9]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
- @Test(groups = { "Functional" })
- public void testGetVisibleContigs()
- {
- HiddenColumns cs = new HiddenColumns();
cs.hideColumns(3, 6);
cs.hideColumns(8, 9);
cs.hideColumns(12, 12);
- // start position is inclusive, end position exclusive:
- int[] visible = cs.getVisibleContigs(1, 13);
- assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 14);
- assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(3, 10);
- assertEquals("[7, 7]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 6);
- assertEquals("[]", Arrays.toString(visible));
+ // Test both ends visible region
+
+ // start position is inclusive, end position exclusive
+ visible = cs.getVisContigsIterator(1, 13, false);
+ region = visible.next();
+ assertEquals("[1, 2]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // Test start hidden, end visible
+ visible = cs.getVisContigsIterator(4, 14, false);
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[13, 13]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // Test start hidden, end hidden
+ visible = cs.getVisContigsIterator(3, 10, false);
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // Test start visible, end hidden
+ visible = cs.getVisContigsIterator(0, 13, false);
+ region = visible.next();
+ assertEquals("[0, 2]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // Test empty result
+ visible = cs.getVisContigsIterator(4, 6, false);
+ assertFalse(visible.hasNext());
}
@Test(groups = { "Functional" })
assertFalse(cs.equals(cs2));
assertFalse(cs2.equals(cs));
+ // with the wrong kind of object
+ assertFalse(cs.equals(new HiddenColumnsCursor()));
+
+ // with a different hiddenColumns object - by size
+ HiddenColumns cs3 = new HiddenColumns();
+ cs3.hideColumns(2, 3);
+ assertFalse(cs.equals(cs3));
+
// with hidden columns added in a different order
cs2.hideColumns(6, 9);
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
cs2.hideColumns(5, 8);
assertTrue(cs.equals(cs2));
assertTrue(cs.equals(cs));
assertTrue(cs2.equals(cs));
assertTrue(cs2.equals(cs2));
+
+ // different ranges, same size
+ cs.hideColumns(10, 12);
+ cs2.hideColumns(10, 15);
+ assertFalse(cs.equals(cs2));
+
}
@Test(groups = "Functional")
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
+ Iterator<int[]> regions = cs.iterator();
assertEquals("[5, 7]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
HiddenColumns cs2 = new HiddenColumns(cs);
+ regions = cs2.iterator();
assertTrue(cs2.hasHiddenColumns());
- assertEquals(2, cs2.getHiddenColumnsCopy().size());
+ assertEquals(2, cs2.getNumberOfRegions());
// hidden columns are held in column order
assertEquals("[5, 7]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
assertEquals("[10, 11]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+ Arrays.toString(regions.next()));
}
- /**
- * Test the code used to locate the reference sequence ruler origin
- */
- @Test(groups = { "Functional" })
- public void testLocateVisibleBoundsofSequence()
+ @Test(groups = "Functional")
+ public void testCopyConstructor2()
{
- // create random alignment
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(10, 11);
+ cs.hideColumns(5, 7);
- HiddenColumns cs = al.getHiddenColumns();
- ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
+ assertTrue(cs2.hasHiddenColumns());
+ Iterator<int[]> regions = cs2.iterator();
- SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
- assertEquals(2, seq.findIndex(seq.getStart()));
-
- // no hidden columns
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- // hidden column on gap after end of sequence - should not affect bounds
- colsel.hideSelectedColumns(13, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ // only [5,7] returned, offset by 1
+ assertEquals("[4, 6]",
+ Arrays.toString(regions.next()));
+ assertEquals(3, cs2.getSize());
- cs.revealAllHiddenColumns(colsel);
- // hidden column on gap before beginning of sequence - should vis bounds by
- // one
- colsel.hideSelectedColumns(0, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
- seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns(colsel);
- // hide columns around most of sequence - leave one residue remaining
- cs.hideColumns(1, 3);
- cs.hideColumns(6, 11);
- assertEquals("-D",
- cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
- assertEquals(
- Arrays.toString(new int[] { 1, 1, 3, 3,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
- cs.revealAllHiddenColumns(colsel);
+ cs2 = new HiddenColumns(cs, 8, 15, 4);
+ regions = cs2.iterator();
+ assertTrue(cs2.hasHiddenColumns());
- // hide whole sequence - should just get location of hidden region
- // containing sequence
- cs.hideColumns(1, 11);
- assertEquals(
- Arrays.toString(new int[] { 0, 1, 0, 0,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+ // only [10,11] returned, offset by 4
+ assertEquals("[6, 7]",
+ Arrays.toString(regions.next()));
+ assertEquals(2, cs2.getSize());
+ cs2 = new HiddenColumns(cs, 6, 10, 4);
+ assertFalse(cs2.hasHiddenColumns());
}
- @Test(groups = { "Functional" })
- public void testLocateVisibleBoundsPathologicals()
- {
- // test some pathological cases we missed
- AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
- "refseqGaptest", "KTDVTI----------NFI-----G----L") });
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(al.getSequenceAt(0));
- assertEquals(
- "G",
- ""
- + al.getSequenceAt(0).getCharAt(
- cs.adjustForHiddenColumns(9)));
-
- }
@Test(groups = { "Functional" })
public void testHideColumns()
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = al.getHiddenColumns();
colsel.hideSelectedColumns(5, al.getHiddenColumns());
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+ Iterator<int[]> regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[5, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 1);
colsel.hideSelectedColumns(3, al.getHiddenColumns());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
+ regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
// two hidden ranges, in order:
- assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
- assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
- assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+ assertEquals("[3, 3]", Arrays.toString(regions.next()));
+ assertEquals("[5, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 2);
// hiding column 4 expands [3, 3] to [3, 4]
// and merges to [5, 5] to make [3, 5]
colsel.hideSelectedColumns(4, al.getHiddenColumns());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[3, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 3);
// clear hidden columns (note they are added to selected)
cs.revealAllHiddenColumns(colsel);
// it is now actually null but getter returns an empty list
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+ assertEquals(0, cs.getNumberOfRegions());
+ assertEquals(cs.getSize(), 0);
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- int[] firstHiddenRange = hidden.get(0);
+ regions = cs.iterator();
+ int[] firstHiddenRange = regions.next();
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
+ assertEquals(cs.getSize(), 4);
// adding a subrange of already hidden should do nothing
cs.hideColumns(4, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(4, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 4]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 3);
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 5]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 4);
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 6]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 5);
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[1, 7]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 7);
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(15, 18);
+ cs.hideColumns(2, 4);
+ cs.hideColumns(7, 9);
+ regions = cs.iterator();
+ assertEquals(3, cs.getNumberOfRegions());
+ assertEquals("[2, 4]", Arrays.toString(regions.next()));
+ assertEquals("[7, 9]", Arrays.toString(regions.next()));
+ assertEquals("[15, 18]", Arrays.toString(regions.next()));
+ assertEquals(cs.getSize(), 10);
}
/**
{
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = new HiddenColumns();
+
+ // test with null hidden columns
+ cs.revealHiddenColumns(5, colsel);
+ assertTrue(colsel.getSelected().isEmpty());
+
cs.hideColumns(5, 8);
colsel.addElement(10);
cs.revealHiddenColumns(5, colsel);
- // hidden columns list now null but getter returns empty list:
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+
+ // hiddenColumns now empty
+ assertEquals(0, cs.getSize());
+
// revealed columns are marked as selected (added to selection):
assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
colsel = new ColumnSelection();
cs = new HiddenColumns();
cs.hideColumns(5, 8);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
+
+ int prevSize = cs.getSize();
cs.revealHiddenColumns(6, colsel);
- assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+ assertEquals(prevSize, cs.getSize());
+ assertTrue(colsel.getSelected().isEmpty());
+
+ // reveal hidden columns when there is more than one region
+ cs.hideColumns(20, 23);
+ // now there are 2 hidden regions
+ assertEquals(2, cs.getNumberOfRegions());
+
+ cs.revealHiddenColumns(20, colsel);
+
+ // hiddenColumns now has one region
+ assertEquals(1, cs.getNumberOfRegions());
+
+ // revealed columns are marked as selected (added to selection):
+ assertEquals("[20, 21, 22, 23]", colsel.getSelected().toString());
+
+ // call with a column past the end of the hidden column ranges
+ colsel.clear();
+ cs.revealHiddenColumns(20, colsel);
+ // hiddenColumns still has 1 region
+ assertEquals(1, cs.getNumberOfRegions());
assertTrue(colsel.getSelected().isEmpty());
}
@Test(groups = { "Functional" })
public void testRevealAllHiddenColumns()
{
- HiddenColumns cs = new HiddenColumns();
+ HiddenColumns hidden = new HiddenColumns();
ColumnSelection colsel = new ColumnSelection();
- cs.hideColumns(5, 8);
- cs.hideColumns(2, 3);
+
+ // test with null hidden columns
+ hidden.revealAllHiddenColumns(colsel);
+ assertTrue(colsel.getSelected().isEmpty());
+
+ hidden.hideColumns(5, 8);
+ hidden.hideColumns(2, 3);
colsel.addElement(11);
colsel.addElement(1);
- cs.revealAllHiddenColumns(colsel);
+ hidden.revealAllHiddenColumns(colsel);
/*
* revealing hidden columns adds them (in order) to the (unordered)
* selection list
*/
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
- assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
- .toString());
+
+ // hiddenColumns now empty
+ assertEquals(0, hidden.getSize());
+
+ assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
+ colsel.getSelected().toString());
}
@Test(groups = { "Functional" })
public void testIsVisible()
{
HiddenColumns cs = new HiddenColumns();
+ assertTrue(cs.isVisible(5));
+
cs.hideColumns(2, 4);
cs.hideColumns(6, 7);
assertTrue(cs.isVisible(0));
assertTrue(cs.isVisible(5));
assertFalse(cs.isVisible(6));
assertFalse(cs.isVisible(7));
+ assertTrue(cs.isVisible(8));
}
/**
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(49, 59);
cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
- assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+ Iterator<int[]> regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals("[49, 59]", Arrays.toString(regions.next()));
+ assertEquals("[69, 79]", Arrays.toString(regions.next()));
+ assertEquals(22, cs.getSize());
cs.hideColumns(48, 80);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[48, 80]", Arrays.toString(regions.next()));
+ assertEquals(33, cs.getSize());
/*
* another...joining hidden ranges
cs.hideColumns(50, 60);
// hiding 21-49 should merge to one range
cs.hideColumns(21, 49);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[10, 60]", Arrays.toString(regions.next()));
+ assertEquals(51, cs.getSize());
/*
* another...left overlap, subsumption, right overlap,
cs.hideColumns(60, 70);
cs.hideColumns(15, 45);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
- assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+ regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals("[10, 50]", Arrays.toString(regions.next()));
+ assertEquals("[60, 70]", Arrays.toString(regions.next()));
+ assertEquals(52, cs.getSize());
}
@Test(groups = { "Functional" })
- public void testHideBitset()
+ public void testHideColumns_BitSet()
{
HiddenColumns cs;
// one hidden range
one.set(1);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(1, cs.getSize());
one.set(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
one.set(3);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals(3, cs.getSize());
// split
one.clear(2);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
- assertEquals(2, cs.getHiddenColumnsCopy().size());
+ cs.hideColumns(one);
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals(2, cs.getSize());
- assertEquals(0, cs.adjustForHiddenColumns(0));
- assertEquals(2, cs.adjustForHiddenColumns(1));
- assertEquals(4, cs.adjustForHiddenColumns(2));
+ assertEquals(0, cs.visibleToAbsoluteColumn(0));
+ assertEquals(2, cs.visibleToAbsoluteColumn(1));
+ assertEquals(4, cs.visibleToAbsoluteColumn(2));
// one again
one.clear(1);
cs = new HiddenColumns();
- cs.hideMarkedBits(one);
+ cs.hideColumns(one);
+ assertEquals(1, cs.getSize());
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
- assertEquals(0, cs.adjustForHiddenColumns(0));
- assertEquals(1, cs.adjustForHiddenColumns(1));
- assertEquals(2, cs.adjustForHiddenColumns(2));
- assertEquals(4, cs.adjustForHiddenColumns(3));
- }
-
- @Test(groups = { "Functional" })
- public void testGetBitset()
- {
- BitSet toMark, fromMark;
- long seed = -3241532;
- Random number = new Random(seed);
- for (int n = 0; n < 1000; n++)
- {
- // create a random bitfield
- toMark = BitSet.valueOf(new long[] { number.nextLong(),
- number.nextLong(), number.nextLong() });
- toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
- HiddenColumns hc = new HiddenColumns();
- hc.hideMarkedBits(toMark);
-
- // see if we can recover bitfield
- hc.markHiddenRegions(fromMark = new BitSet());
- assertEquals(toMark, fromMark);
- }
- }
-
- @Test(groups = { "Functional" })
- public void testFindHiddenRegionPositions()
- {
- HiddenColumns hc = new HiddenColumns();
-
- List<Integer> positions = hc.findHiddenRegionPositions();
- assertTrue(positions.isEmpty());
-
- hc.hideColumns(3, 7);
- hc.hideColumns(10, 10);
- hc.hideColumns(14, 15);
-
- positions = hc.findHiddenRegionPositions();
- assertEquals(3, positions.size());
- assertEquals(3, positions.get(0).intValue());
- assertEquals(5, positions.get(1).intValue());
- assertEquals(8, positions.get(2).intValue());
+ assertEquals(0, cs.visibleToAbsoluteColumn(0));
+ assertEquals(1, cs.visibleToAbsoluteColumn(1));
+ assertEquals(2, cs.visibleToAbsoluteColumn(2));
+ assertEquals(4, cs.visibleToAbsoluteColumn(3));
}
@Test(groups = { "Functional" })
}
@Test(groups = "Functional")
- public void getVisibleStartAndEndIndexTest()
+ public void testGetVisibleStartAndEndIndex()
{
Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
AlignmentI align = new Alignment(new SequenceI[] { seq });
System.out.println(startEnd[0] + " : " + startEnd[1]);
assertEquals(1, startEnd[0]);
assertEquals(23, startEnd[1]);
+
+ // force lowest range to start of alignment
+ hc = new HiddenColumns();
+ hc.hideColumns(3, 4);
+ startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+ assertEquals(0, startEnd[0]);
+ assertEquals(25, startEnd[1]);
}
@Test(groups = "Functional")
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
- result = hc.getRegionWithEdgeAtRes(3);
+ result = hc.getRegionWithEdgeAtRes(2);
assertEquals(3, result[0]);
assertEquals(7, result[1]);
+ result = hc.getRegionWithEdgeAtRes(4);
+ assertEquals(10, result[0]);
+ assertEquals(10, result[1]);
+
result = hc.getRegionWithEdgeAtRes(5);
assertEquals(10, result[0]);
assertEquals(10, result[1]);
result = hc.getRegionWithEdgeAtRes(6);
assertNull(result);
+
+ result = hc.getRegionWithEdgeAtRes(0);
+ assertNull(result);
+
+ result = hc.getRegionWithEdgeAtRes(7);
+ assertEquals(14, result[0]);
+ assertEquals(15, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(8);
+ assertEquals(14, result[0]);
+ assertEquals(15, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(16);
+ assertNull(result);
}
@Test(groups = "Functional")
- public void testPropagateInsertions()
+ public void testHasHiddenColumns()
{
- // create an alignment with no gaps - this will be the profile seq and other
- // JPRED seqs
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
-
- // get the profileseq
- SequenceI profileseq = al.getSequenceAt(0);
- SequenceI gappedseq = new Sequence(profileseq);
- gappedseq.insertCharAt(5, al.getGapCharacter());
- gappedseq.insertCharAt(6, al.getGapCharacter());
- gappedseq.insertCharAt(7, al.getGapCharacter());
- gappedseq.insertCharAt(8, al.getGapCharacter());
-
- // create an alignment view with the gapped sequence
- SequenceI[] seqs = new SequenceI[1];
- seqs[0] = gappedseq;
- AlignmentI newal = new Alignment(seqs);
- HiddenColumns hidden = new HiddenColumns();
- hidden.hideColumns(15, 17);
-
- AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
- false);
-
- // confirm that original contigs are as expected
- int[] oldcontigs = hidden.getVisibleContigs(0, 20);
- int[] testcontigs = { 0, 14, 18, 19 };
- assertTrue(Arrays.equals(oldcontigs, testcontigs));
-
- // propagate insertions
- HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
- view);
-
- // confirm that the contigs have changed to account for the gaps
- int[] newcontigs = result.getVisibleContigs(0, 20);
- testcontigs[1] = 10;
- testcontigs[2] = 14;
- assertTrue(Arrays.equals(newcontigs, testcontigs));
-
+ HiddenColumns h = new HiddenColumns();
+
+ // new HiddenColumns2 has no hidden cols
+ assertFalse(h.hasHiddenColumns());
+
+ // some columns hidden, returns true
+ h.hideColumns(5, 10);
+ assertTrue(h.hasHiddenColumns());
+
+ // reveal columns, no hidden cols again
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ assertFalse(h.hasHiddenColumns());
+ }
+
+ @Test(groups = "Functional")
+ public void testHasManyHiddenColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // h has no hidden cols
+ assertFalse(h.hasMultiHiddenColumnRegions());
+
+ // one set of columns hidden, returns false
+ h.hideColumns(5, 10);
+ assertFalse(h.hasMultiHiddenColumnRegions());
+
+ // two sets hidden, returns true
+ h.hideColumns(15, 17);
+ assertTrue(h.hasMultiHiddenColumnRegions());
+
+ // back to one block, asserts false
+ h.hideColumns(11, 14);
+ assertFalse(h.hasMultiHiddenColumnRegions());
+ }
+
+ @Test(groups = "Functional")
+ public void testAdjustForHiddenColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+ // returns input value when there are no hidden columns
+ assertEquals(10, h.visibleToAbsoluteColumn(10));
+
+ h.hideColumns(20, 30);
+ assertEquals(10, h.visibleToAbsoluteColumn(10));
+ assertEquals(20 + 11, h.visibleToAbsoluteColumn(20));
+ assertEquals(35 + 11, h.visibleToAbsoluteColumn(35));
+
+ h.hideColumns(5, 7);
+ assertEquals(10 + 3, h.visibleToAbsoluteColumn(10));
+ assertEquals(20 + 14, h.visibleToAbsoluteColumn(20));
+ assertEquals(35 + 14, h.visibleToAbsoluteColumn(35));
+
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 1);
+ assertEquals(4, h.visibleToAbsoluteColumn(2));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetNextHiddenBoundary_Left()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // returns same value if no hidden cols
+ assertEquals(3, h.getNextHiddenBoundary(true, 3));
+
+ h.hideColumns(5, 10);
+ assertEquals(10, h.getNextHiddenBoundary(true, 15));
+ assertEquals(3, h.getNextHiddenBoundary(true, 3));
+ assertEquals(7, h.getNextHiddenBoundary(true, 7));
+
+ h.hideColumns(15, 20);
+ assertEquals(10, h.getNextHiddenBoundary(true, 15));
+ assertEquals(20, h.getNextHiddenBoundary(true, 21));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetNextHiddenBoundary_Right()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // returns same value if no hidden cols
+ assertEquals(3, h.getNextHiddenBoundary(false, 3));
+
+ h.hideColumns(5, 10);
+ assertEquals(5, h.getNextHiddenBoundary(false, 3));
+ assertEquals(15, h.getNextHiddenBoundary(false, 15));
+ assertEquals(7, h.getNextHiddenBoundary(false, 7));
+
+ h.hideColumns(15, 20);
+ assertEquals(15, h.getNextHiddenBoundary(false, 7));
+ assertEquals(15, h.getNextHiddenBoundary(false, 14));
+
+ // returns same value if there is no next hidden column
+ assertEquals(22, h.getNextHiddenBoundary(false, 22));
+ }
+
+ @Test(groups = "Functional")
+ public void testIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<int[]> result = h.iterator();
+ assertFalse(result.hasNext());
+
+ h.hideColumns(5, 10);
+ result = h.iterator();
+ int[] next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ assertFalse(result.hasNext());
+
+ h.hideColumns(22, 23);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ next = result.next();
+ assertEquals(22, next[0]);
+ assertEquals(23, next[1]);
+ assertFalse(result.hasNext());
+
+ // test for only one hidden region at start of alignment
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 1);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(0, next[0]);
+ assertEquals(1, next[1]);
+ assertFalse(result.hasNext());
+ }
+
+ /* @Test(groups = "Functional")
+ public void testGetVisibleSequenceStrings()
+ {
+ HiddenColumns h = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+ SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
+ SequenceI[] seqs = new SequenceI[2];
+ seqs[0] = seq1;
+ seqs[1] = seq2;
+ String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WKQES", result[0]);
+ assertEquals("RNDTG", result[1]);
+
+ h.hideColumns(6, 8);
+ result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WS", result[0]);
+ assertEquals("RG", result[1]);
+
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(1, 3);
+ h.hideColumns(6, 11);
+ assertEquals("-D",
+ h.getVisibleSequenceStrings(0, 5, new SequenceI[]
+ { seq })[0]);
+ }*/
+
+ @Test(groups = "Functional")
+ public void testHideInsertionsFor()
+ {
+ HiddenColumns h = new HiddenColumns();
+ HiddenColumns h2 = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
+ SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+
+ h.hideList(seq2.getInsertions());
+ assertTrue(h.equals(h2));
+ assertEquals(0, h.getSize());
+
+ h.hideList(seq1.getInsertions());
+ h2.hideColumns(3, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(19, 20);
+ assertTrue(h.equals(h2));
+ assertEquals(6, h.getSize());
+ }
+
+ @Test(groups = "Functional")
+ public void testHideColumns_BitSet_range()
+ {
+ HiddenColumns h = new HiddenColumns();
+ HiddenColumns h2 = new HiddenColumns();
+
+ BitSet tohide = new BitSet(25);
+ h.hideColumns(tohide);
+ assertTrue(h.equals(h2));
+
+ // when setting bitset, first param is inclusive, second exclusive
+ tohide.set(3, 6);
+ tohide.set(9);
+ tohide.set(15, 21);
+ h.clearAndHideColumns(tohide, 5, 23);
+
+ h2.hideColumns(5, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(15, 20);
+ assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
+
+ tohide.clear();
+ tohide.set(41);
+ h.clearAndHideColumns(tohide, 23, 30);
+ assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
+
+ tohide.set(41);
+ h.clearAndHideColumns(tohide, 30, 45);
+ h2.hideColumns(41, 41);
+ assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
+
+ tohide.clear();
+ tohide.set(25, 28);
+ h.clearAndHideColumns(tohide, 17, 50);
+ h2 = new HiddenColumns();
+ h2.hideColumns(5, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(15, 16);
+ h2.hideColumns(25, 27);
+ assertTrue(h.equals(h2));
+ assertEquals(h.getSize(), h2.getSize());
+
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(3, 5);
+ hc.hideColumns(15, 20);
+ hc.hideColumns(45, 60);
+
+ tohide = new BitSet();
+
+ // all unhidden if tohide is empty and range covers hidden
+ hc.clearAndHideColumns(tohide, 1, 70);
+ assertTrue(!hc.hasHiddenColumns());
+ assertEquals(0, hc.getSize());
+
+ hc.hideColumns(3, 5);
+ hc.hideColumns(15, 20);
+ hc.hideColumns(45, 60);
+ assertEquals(25, hc.getSize());
+
+ // but not if range does not cover hidden
+ hc.clearAndHideColumns(tohide, 23, 40);
+ assertTrue(hc.hasHiddenColumns());
+ assertEquals(25, hc.getSize());
+
+ // and partial unhide if range partially covers
+ hc.clearAndHideColumns(tohide, 1, 17);
+ Iterator<int[]> it = hc.iterator();
+ assertTrue(it.hasNext());
+ int[] region = it.next();
+
+ assertEquals(18, region[0]);
+ assertEquals(20, region[1]);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+
+ assertEquals(45, region[0]);
+ assertEquals(60, region[1]);
+
+ assertFalse(it.hasNext());
+ assertEquals(19, hc.getSize());
+ }
+
+ @Test(groups = "Functional")
+ public void testOffsetByVisibleColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+ int result = h.offsetByVisibleColumns(-1, 10);
+ assertEquals(9, result);
+
+ h.hideColumns(7, 9);
+ result = h.offsetByVisibleColumns(-4, 10);
+ assertEquals(3, result);
+
+ h.hideColumns(14, 15);
+ result = h.offsetByVisibleColumns(-4, 10);
+ assertEquals(3, result);
+
+ result = h.offsetByVisibleColumns(-10, 17);
+ assertEquals(2, result);
+
+ result = h.offsetByVisibleColumns(-1, 7);
+ assertEquals(5, result);
+
+ result = h.offsetByVisibleColumns(-1, 8);
+ assertEquals(5, result);
+
+ result = h.offsetByVisibleColumns(-3, 15);
+ assertEquals(10, result);
+
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 30);
+ result = h.offsetByVisibleColumns(-31, 0);
+ assertEquals(-31, result);
+
+ HiddenColumns cs = new HiddenColumns();
+
+ // test that without hidden columns, offsetByVisibleColumns returns
+ // position n to left of provided position
+ long pos = cs.offsetByVisibleColumns(-3, 10);
+ assertEquals(7, pos);
+
+ // 0 returns same position
+ pos = cs.offsetByVisibleColumns(0, 10);
+ assertEquals(10, pos);
+
+ // overflow to left returns negative number
+ pos = cs.offsetByVisibleColumns(-3, 0);
+ assertEquals(-3, pos);
+
+ // test that with hidden columns to left of result column
+ // behaviour is the same as above
+ cs.hideColumns(1, 3);
+
+ // position n to left of provided position
+ pos = cs.offsetByVisibleColumns(-3, 10);
+ assertEquals(7, pos);
+
+ // 0 returns same position
+ pos = cs.offsetByVisibleColumns(0, 10);
+ assertEquals(10, pos);
+
+ // test with one set of hidden columns between start and required position
+ cs.hideColumns(12, 15);
+ pos = cs.offsetByVisibleColumns(-8, 17);
+ assertEquals(5, pos);
+
+ // test with two sets of hidden columns between start and required position
+ cs.hideColumns(20, 21);
+ pos = cs.offsetByVisibleColumns(-8, 23);
+ assertEquals(9, pos);
+
+ // repeat last 2 tests with no hidden columns to left of required position
+ ColumnSelection colsel = new ColumnSelection();
+ cs.revealAllHiddenColumns(colsel);
+
+ // test with one set of hidden columns between start and required position
+ cs.hideColumns(12, 15);
+ pos = cs.offsetByVisibleColumns(-8, 17);
+ assertEquals(5, pos);
+
+ // test with two sets of hidden columns between start and required position
+ cs.hideColumns(20, 21);
+ pos = cs.offsetByVisibleColumns(-8, 23);
+ assertEquals(9, pos);
+
+ // test with right (positive) offsets
+
+ // test that without hidden columns, offsetByVisibleColumns returns
+ // position n to right of provided position
+ pos = cs.offsetByVisibleColumns(3, 7);
+ assertEquals(10, pos);
+
+ // test that with hidden columns to left of result column
+ // behaviour is the same as above
+ cs.hideColumns(1, 3);
+
+ // test with one set of hidden columns between start and required position
+ cs.hideColumns(12, 15);
+ pos = cs.offsetByVisibleColumns(8, 5);
+ assertEquals(17, pos);
+
+ // test with two sets of hidden columns between start and required position
+ cs.hideColumns(20, 21);
+ pos = cs.offsetByVisibleColumns(8, 9);
+ assertEquals(23, pos);
+
+ // repeat last 2 tests with no hidden columns to left of required position
+ colsel = new ColumnSelection();
+ cs.revealAllHiddenColumns(colsel);
+
+ // test with one set of hidden columns between start and required position
+ cs.hideColumns(12, 15);
+ pos = cs.offsetByVisibleColumns(8, 5);
+ assertEquals(17, pos);
+
+ // test with two sets of hidden columns between start and required position
+ cs.hideColumns(20, 21);
+ pos = cs.offsetByVisibleColumns(8, 9);
+ assertEquals(23, pos);
+ }
+
+ @Test(groups = "Functional")
+ public void testBoundedIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<int[]> it = h.getBoundedIterator(0, 10);
+
+ // no hidden columns = nothing to iterate over
+ assertFalse(it.hasNext());
+
+ // [start,end] contains all hidden columns
+ // all regions are returned
+ h.hideColumns(3, 10);
+ h.hideColumns(14, 16);
+ it = h.getBoundedIterator(0, 20);
+ assertTrue(it.hasNext());
+ int[] next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] overlaps a region
+ // 1 region returned
+ it = h.getBoundedIterator(5, 7);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] fully contains 1 region and start of last
+ // - 2 regions returned
+ it = h.getBoundedIterator(3, 15);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+
+ // [start,end] contains end of first region and whole of last region
+ // - 2 regions returned
+ it = h.getBoundedIterator(4, 20);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next[0]);
+ assertEquals(10, next[1]);
+ next = it.next();
+ assertEquals(14, next[0]);
+ assertEquals(16, next[1]);
+ assertFalse(it.hasNext());
+ }
+
+ @Test(groups = "Functional")
+ public void testBoundedStartIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<Integer> it = h.getStartRegionIterator(0, 10);
+
+ // no hidden columns = nothing to iterate over
+ assertFalse(it.hasNext());
+
+ // [start,end] contains all hidden columns
+ // all regions are returned
+ h.hideColumns(3, 10);
+ h.hideColumns(14, 16);
+ it = h.getStartRegionIterator(0, 20);
+ assertTrue(it.hasNext());
+ int next = it.next();
+ assertEquals(3, next);
+ next = it.next();
+ assertEquals(6, next);
+ assertFalse(it.hasNext());
+
+ // [start,end] does not contain a start of a region
+ // no regions to iterate over
+ it = h.getStartRegionIterator(4, 5);
+ assertFalse(it.hasNext());
+
+ // [start,end] fully contains 1 region and start of last
+ // - 2 regions returned
+ it = h.getStartRegionIterator(3, 7);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(3, next);
+ next = it.next();
+ assertEquals(6, next);
+ assertFalse(it.hasNext());
+
+ // [start,end] contains whole of last region
+ // - 1 region returned
+ it = h.getStartRegionIterator(4, 20);
+ assertTrue(it.hasNext());
+ next = it.next();
+ assertEquals(6, next);
+ assertFalse(it.hasNext());
+ }
+
+ @Test(groups = "Functional")
+ public void testVisibleBlocksVisBoundsIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<int[]> regions = h.getVisContigsIterator(0, 31, true);
+
+ // only 1 visible region spanning 0-30 if nothing is hidden
+ assertTrue(regions.hasNext());
+ int[] region = regions.next();
+ assertEquals(0, region[0]);
+ assertEquals(30, region[1]);
+ assertFalse(regions.hasNext());
+
+ // hide 1 region in middle
+ // 2 regions one on either side
+ // second region boundary accounts for hidden columns
+ h.hideColumns(10, 15);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(0, region[0]);
+ assertEquals(9, region[1]);
+ region = regions.next();
+ assertEquals(16, region[0]);
+ assertEquals(36, region[1]);
+ assertFalse(regions.hasNext());
+
+ // single hidden region at left
+ h = new HiddenColumns();
+ h.hideColumns(0, 5);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(6, region[0]);
+ assertEquals(36, region[1]);
+ assertFalse(regions.hasNext());
+
+ // single hidden region at right
+ h = new HiddenColumns();
+ h.hideColumns(27, 30);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(0, region[0]);
+ assertEquals(26, region[1]);
+ region = regions.next();
+ assertEquals(31, region[0]);
+ assertEquals(34, region[1]);
+ assertFalse(regions.hasNext());
+
+ // hidden region at left + hidden region in middle
+ h = new HiddenColumns();
+ h.hideColumns(0, 5);
+ h.hideColumns(23, 25);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(6, region[0]);
+ assertEquals(22, region[1]);
+ region = regions.next();
+ assertEquals(26, region[0]);
+ assertEquals(39, region[1]);
+ assertFalse(regions.hasNext());
+
+ // hidden region at right + hidden region in middle
+ h = new HiddenColumns();
+ h.hideColumns(27, 30);
+ h.hideColumns(11, 14);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(0, region[0]);
+ assertEquals(10, region[1]);
+ region = regions.next();
+ assertEquals(15, region[0]);
+ assertEquals(26, region[1]);
+ region = regions.next();
+ assertEquals(31, region[0]);
+ assertEquals(38, region[1]);
+ assertFalse(regions.hasNext());
+
+ // hidden region at left and right
+ h = new HiddenColumns();
+ h.hideColumns(27, 35);
+ h.hideColumns(0, 4);
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(5, region[0]);
+ assertEquals(26, region[1]);
+ region = regions.next();
+ assertEquals(36, region[0]);
+ assertEquals(44, region[1]);
+ assertFalse(regions.hasNext());
+
+ // multiple hidden regions
+ h = new HiddenColumns();
+ h.hideColumns(1, 1);
+ h.hideColumns(3, 5);
+ h.hideColumns(9, 11);
+ h.hideColumns(22, 26);
+
+ regions = h.getVisContigsIterator(0, 31, true);
+
+ assertTrue(regions.hasNext());
+ region = regions.next();
+ assertEquals(0, region[0]);
+ assertEquals(0, region[1]);
+ region = regions.next();
+ assertEquals(2, region[0]);
+ assertEquals(2, region[1]);
+ region = regions.next();
+ assertEquals(6, region[0]);
+ assertEquals(8, region[1]);
+ region = regions.next();
+ assertEquals(12, region[0]);
+ assertEquals(21, region[1]);
+ region = regions.next();
+ assertEquals(27, region[0]);
+ assertEquals(42, region[1]);
+ assertFalse(regions.hasNext());
+ }
+
+ /*
+ * the VisibleColsIterator is tested elsewhere, this just tests that
+ * it can be retrieved from HiddenColumns
+ */
+ @Test(groups = "Functional")
+ public void testGetVisibleColsIterator()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Iterator<Integer> it = h.getVisibleColsIterator(0, 10);
+
+ assertTrue(it instanceof RangeElementsIterator);
+ }
+
+ @Test(groups = "Functional")
+ public void testHashCode()
+ {
+ HiddenColumns h = new HiddenColumns();
+ h.hideColumns(0, 25);
+
+ int result = h.hashCode();
+ assertTrue(result > 0);
+
+ h.hideColumns(30, 50);
+ assertTrue(h.hashCode() > 0);
+ assertTrue(result != h.hashCode());
}
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HiddenMarkovModelTest {
+
+ HiddenMarkovModel hmm;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws MalformedURLException, IOException
+ {
+ /*
+ * load hmm model of a Kinase domain to a HiddenMarkovModel
+ */
+ HMMFile file = new HMMFile(new FileParse(
+ "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+ hmm = file.getHMM();
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMatchEmissionProbabilities()
+ throws MalformedURLException, IOException
+ {
+ /*
+ * raw value in file is 3.67403
+ * saved as probability e^-X = 0.05259
+ */
+ double mep = hmm.getMatchEmissionProbability(0, 'R');
+ assertEquals(mep, 0.02537400637, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -3.67403), 0.0001d);
+
+ mep = hmm.getMatchEmissionProbability(19, 'W');
+ assertEquals(mep, 0.00588228492, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -5.13581), 0.0001d);
+
+ // column 160 is a gapped region of the model
+ mep = hmm.getMatchEmissionProbability(160, 'G');
+ assertEquals(mep, 0D, 0.0001d);
+
+ mep = hmm.getMatchEmissionProbability(475, 'A');
+ assertEquals(mep, 0.04995163708, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -2.99670), 0.0001d);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetInsertEmissionProbabilities()
+ {
+ double iep = hmm.getInsertEmissionProbability(2, 'A');
+ assertEquals(iep, Math.pow(Math.E, -2.68618), 0.0001d);
+ // symbol is not case-sensitive
+ assertEquals(iep, hmm.getInsertEmissionProbability(2, 'a'));
+
+ iep = hmm.getInsertEmissionProbability(5, 'T');
+ assertEquals(iep, Math.pow(Math.E, -2.77519), 0.0001d);
+
+ // column 161 is gapped in the hmm
+ iep = hmm.getInsertEmissionProbability(161, 'K');
+ assertEquals(iep, 0D, 0.0001d);
+
+ iep = hmm.getInsertEmissionProbability(472, 'L');
+ assertEquals(iep, Math.pow(Math.E, -2.69355), 0.0001d);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetStateTransitionProbabilities()
+ {
+ // * in model file treated as negative infinity
+ double stp = hmm.getStateTransitionProbability(475,
+ HiddenMarkovModel.MATCHTODELETE);
+ assertEquals(stp, Double.NEGATIVE_INFINITY);
+
+ // file value is 5.01631, saved as e^-5.01631
+ stp = hmm.getStateTransitionProbability(8,
+ HiddenMarkovModel.MATCHTOINSERT);
+ assertEquals(stp, Math.pow(Math.E, -5.01631), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(36,
+ HiddenMarkovModel.MATCHTODELETE);
+ assertEquals(stp, Math.pow(Math.E, -5.73865), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(22,
+ HiddenMarkovModel.INSERTTOMATCH);
+ assertEquals(stp, Math.pow(Math.E, -0.61958), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(80,
+ HiddenMarkovModel.INSERTTOINSERT);
+ assertEquals(stp, Math.pow(Math.E, -0.77255), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(475,
+ HiddenMarkovModel.DELETETOMATCH);
+ assertEquals(stp, 1D, 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(218,
+ HiddenMarkovModel.DELETETODELETE);
+ assertEquals(stp, Math.pow(Math.E, -0.95510), 0.0001D);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetConsensusSequence()
+ {
+ SequenceI seq = hmm.getConsensusSequence();
+ String subStr = seq.getSequenceAsString().substring(0, 10);
+ assertEquals(subStr, "yelleklGsG");
+ subStr = seq.getSequenceAsString().substring(150, 161);
+ assertEquals(subStr, "-dllk------");
+ }
+
+ /**
+ * A rather pointless test that reproduces the code implemented and asserts
+ * the result is the same...
+ */
+ @Test(groups = "Functional")
+ public void testGetInformationContent()
+ {
+ /*
+ * information measure is sum over all symbols of
+ * emissionProb * log(emissionProb / background) / log(2)
+ */
+ Map<Character, Float> uniprotFreqs = ResidueProperties.backgroundFrequencies
+ .get("amino");
+ int col = 4;
+ float expected = 0f;
+ for (char aa : hmm.getSymbols().toCharArray())
+ {
+ double mep = hmm.getMatchEmissionProbability(col, aa);
+ float background = uniprotFreqs.get(aa);
+ expected += mep * Math.log(mep / background);
+ }
+ expected /= Math.log(2D);
+
+ float actual = hmm.getInformationContent(col);
+ assertEquals(actual, expected, 0.0001d);
+ }
+}
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
+import jalview.viewmodel.AlignmentViewport;
import java.util.List;
* represent seqs 2-4 with seq3
* this hides seq2 and seq4 but not seq3
*/
- AlignViewport av = new AlignViewport(al);
+ AlignmentViewport av = new AlignViewport(al);
SequenceGroup sg = new SequenceGroup();
sg.addSequence(seqs[1], false);
sg.addSequence(seqs[2], false);
import static org.testng.Assert.assertTrue;
+import java.util.Iterator;
import java.util.NoSuchElementException;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-public class VisibleColsIteratorTest
+public class RangeElementsIteratorTest
{
HiddenColumns hiddenCols;
@Test(groups = { "Functional" })
public void testHasNextAndNextWithHidden()
{
- VisibleColsIterator it = new VisibleColsIterator(0, 6, hiddenCols);
+ Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 6);
int count = 0;
while (it.hasNext())
{
- it.next();
+ int result = it.next();
+ System.out.println(result);
count++;
}
assertTrue(count == 4, "hasNext() is false after 4 iterations");
@Test(groups = { "Functional" })
public void testHasNextAndNextNoHidden()
{
- VisibleColsIterator it2 = new VisibleColsIterator(0, 3,
- new HiddenColumns());
+ HiddenColumns test = new HiddenColumns();
+ Iterator<Integer> it2 = test.getVisibleColsIterator(0, 3);
int count = 0;
while (it2.hasNext())
{
@Test(groups = { "Functional" })
public void testHasNextAndNextStartHidden()
{
- VisibleColsIterator it3 = new VisibleColsIterator(0, 6,
- hiddenColsAtStart);
+ Iterator<Integer> it3 = hiddenColsAtStart.getVisibleColsIterator(0, 6);
int count = 0;
while (it3.hasNext())
{
@Test(groups = { "Functional" })
public void testHasNextAndNextEndHidden()
{
- VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols);
+ Iterator<Integer> it4 = hiddenCols.getVisibleColsIterator(0, 4);
int count = 0;
while (it4.hasNext())
{
expectedExceptions = { NoSuchElementException.class })
public void testLastNextWithHidden() throws NoSuchElementException
{
- VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols);
+ Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
while (it.hasNext())
{
it.next();
expectedExceptions = { NoSuchElementException.class })
public void testLastNextNoHidden() throws NoSuchElementException
{
- VisibleColsIterator it2 = new VisibleColsIterator(0, 3,
- new HiddenColumns());
+ HiddenColumns test = new HiddenColumns();
+ Iterator<Integer> it2 = test.getVisibleColsIterator(0, 3);
while (it2.hasNext())
{
it2.next();
expectedExceptions = { NoSuchElementException.class })
public void testLastNextStartHidden() throws NoSuchElementException
{
- VisibleColsIterator it3 = new VisibleColsIterator(0, 6,
- hiddenColsAtStart);
+ Iterator<Integer> it3 = hiddenColsAtStart.getVisibleColsIterator(0, 6);
while (it3.hasNext())
{
it3.next();
expectedExceptions = { NoSuchElementException.class })
public void testLastNextEndHidden() throws NoSuchElementException
{
- VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols);
+ Iterator<Integer> it4 = hiddenCols.getVisibleColsIterator(0, 4);
while (it4.hasNext())
{
it4.next();
expectedExceptions = { UnsupportedOperationException.class })
public void testRemove() throws UnsupportedOperationException
{
- VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols);
+ Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
it.remove();
}
}
import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.gui.JvOptionPane;
+import java.util.Arrays;
+
import org.junit.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
assertEquals(rc.getCount('N'), 1);
assertEquals(rc.getCount('?'), 0);
assertEquals(rc.getCount('-'), 0);
+ assertEquals(rc.getTotalResidueCount(), 11);
assertFalse(rc.isCountingInts());
assertFalse(rc.isUsingOtherData());
assertEquals(rc.getCount(' '), 4);
assertEquals(rc.getCount('-'), 4);
assertEquals(rc.getCount('.'), 4);
+ assertEquals(rc.getTotalResidueCount(), 0);
assertFalse(rc.isUsingOtherData());
assertFalse(rc.isCountingInts());
}
assertEquals(rc.getCount('m'), 13);
assertEquals(rc.getCount('G'), 0);
assertEquals(rc.getCount('-'), 0);
+ assertEquals(rc.getTotalResidueCount(), 27);
assertFalse(rc.isCountingInts());
assertFalse(rc.isUsingOtherData());
assertEquals(rc.getCount('?'), 6);
assertEquals(rc.getCount('!'), 7);
}
+
+ @Test(groups = "Functional")
+ public void testConstructor_forSequences()
+ {
+ SequenceI seq1 = new Sequence("seq1", "abcde--. FCD");
+ SequenceI seq2 = new Sequence("seq2", "ab.kKqBd-.");
+ ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2));
+
+ assertEquals(rc.getGapCount(), 7);
+ assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps
+ assertEquals(rc.getCount('a'), 2);
+ assertEquals(rc.getCount('A'), 2);
+ assertEquals(rc.getCount('B'), 3);
+ assertEquals(rc.getCount('c'), 2);
+ assertEquals(rc.getCount('D'), 3);
+ assertEquals(rc.getCount('f'), 1);
+ assertEquals(rc.getCount('K'), 2);
+ assertEquals(rc.getCount('Q'), 1);
+ }
}
import java.awt.Color;
import java.util.Collections;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceGroupTest
{
@Test(groups={"Functional"})
sg.setDisplayBoxes(false);
sg.setDisplayText(false);
sg.setColourText(true);
- sg.isDefined = true;
+ PA.setValue(sg, "isDefined", true);
sg.setShowNonconserved(true);
sg.setOutlineColour(Color.red);
sg.setIdColour(Color.blue);
assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
assertEquals(sg2.textColour, sg.textColour);
assertEquals(sg2.textColour2, sg.textColour2);
- assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
+ assertEquals(sg2.isIgnoreGapsConsensus(), sg.isIgnoreGapsConsensus());
assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
assertEquals(sg2.isNormaliseSequenceLogo(),
sg.isNormaliseSequenceLogo());
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentGenerator;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.PDBEntry.Type;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Vector;
-import junit.extensions.PA;
-
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceTest
{
Assert.assertEquals(pdbe1a,
sq.getDatasetSequence().getPDBEntry("1PDB"),
"PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
- ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+ ArrayList<Annotation> annotsList = new ArrayList<>();
System.out.println(">>>>>> " + sq.getSequenceAsString().length());
annotsList.add(new Annotation("A", "A", 'X', 0.1f));
annotsList.add(new Annotation("A", "A", 'X', 0.1f));
}
@Test(groups = { "Functional" })
+ public void testGapBitset()
+ {
+ SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+ BitSet bs = sq.gapBitset();
+ BitSet expected = new BitSet();
+ expected.set(0);
+ expected.set(4, 7);
+ expected.set(9);
+ expected.set(11, 13);
+
+ assertTrue(bs.equals(expected));
+
+ }
+
public void testFindFeatures_largeEndPos()
{
/*
assertEquals(8, sq.getDatasetSequence().getStart());
assertEquals(9, sq.getDatasetSequence().getEnd());
}
+
+ /**
+ * Test the code used to locate the reference sequence ruler origin
+ */
+ @Test(groups = { "Functional" })
+ public void testLocateVisibleStartofSequence()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ HiddenColumns cs = al.getHiddenColumns();
+ ColumnSelection colsel = new ColumnSelection();
+
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ assertEquals(2, seq.findIndex(seq.getStart()));
+
+ // no hidden columns
+ assertEquals(seq.findIndex(seq.getStart()) - 1,
+ seq.firstResidueOutsideIterator(cs.iterator()));
+
+ // hidden column on gap after end of sequence - should not affect bounds
+ colsel.hideSelectedColumns(13, al.getHiddenColumns());
+ assertEquals(seq.findIndex(seq.getStart()) - 1,
+ seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ // hidden column on gap before beginning of sequence - should vis bounds by
+ // one
+ colsel.hideSelectedColumns(0, al.getHiddenColumns());
+ assertEquals(seq.findIndex(seq.getStart()) - 2,
+ cs.absoluteToVisibleColumn(
+ seq.firstResidueOutsideIterator(cs.iterator())));
+
+ cs.revealAllHiddenColumns(colsel);
+ // hide columns around most of sequence - leave one residue remaining
+ cs.hideColumns(1, 3);
+ cs.hideColumns(6, 11);
+
+ Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
+
+ assertEquals("-D", seq.getSequenceStringFromIterator(it));
+ // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
+ // { seq })[0]);
+
+ assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+ cs.revealAllHiddenColumns(colsel);
+
+ // hide whole sequence - should just get location of hidden region
+ // containing sequence
+ cs.hideColumns(1, 11);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 15);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(7, 17);
+ assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 17);
+ assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 19);
+ assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 0);
+ assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 1);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 2);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(1, 1);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(1, 2);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(1, 3);
+ assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 2);
+ cs.hideColumns(5, 6);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 2);
+ cs.hideColumns(5, 6);
+ cs.hideColumns(9, 10);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 2);
+ cs.hideColumns(7, 11);
+ assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(2, 4);
+ cs.hideColumns(7, 11);
+ assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(2, 4);
+ cs.hideColumns(7, 12);
+ assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(1, 11);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 12);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 4);
+ cs.hideColumns(6, 12);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 1);
+ cs.hideColumns(3, 12);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 14);
+ cs.hideColumns(17, 19);
+ assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 7);
+ cs.hideColumns(9, 14);
+ cs.hideColumns(17, 19);
+ assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 1);
+ cs.hideColumns(3, 4);
+ cs.hideColumns(6, 8);
+ cs.hideColumns(10, 12);
+ assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+ }
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class StartRegionIteratorTest
+{
+ /**
+ * Test the start region iterator
+ */
+ @Test(groups = { "Functional" })
+ public void testBasicBoundsIterator()
+ {
+ List<int[]> hiddenColumns = null;
+
+ // null hidden columns
+ Iterator<Integer> it = new StartRegionIterator(3, 10,
+ hiddenColumns);
+ assertFalse(it.hasNext());
+
+ hiddenColumns = new ArrayList<>();
+
+ // no hidden columns
+ it = new StartRegionIterator(3, 10, hiddenColumns);
+ assertFalse(it.hasNext());
+
+ // add some hidden columns
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ it = new StartRegionIterator(3, 10, hiddenColumns);
+ assertTrue(it.hasNext());
+ Integer result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(3, 15, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(3, 18, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(3, 19, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertFalse(it.hasNext());
+
+ hiddenColumns.add(new int[] { 47, 50 });
+
+ it = new StartRegionIterator(15, 60, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(25, (int) result);
+ assertFalse(it.hasNext());
+ }
+
+ /**
+ * Test the start region iterator with null cursor
+ */
+ @Test(groups = { "Functional" })
+ public void testBoundsIteratorUsingNullCursor()
+ {
+ List<int[]> hiddenColumns = null;
+ HiddenCursorPosition pos = null;
+
+ // null hidden columns
+ Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
+ hiddenColumns);
+ assertFalse(it.hasNext());
+
+ hiddenColumns = new ArrayList<>();
+
+ // no hidden columns
+ it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
+ assertFalse(it.hasNext());
+
+ // add some hidden columns
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
+ assertTrue(it.hasNext());
+ Integer result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertFalse(it.hasNext());
+
+ hiddenColumns.add(new int[] { 47, 50 });
+
+ it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(25, (int) result);
+ assertFalse(it.hasNext());
+ }
+
+ /**
+ * Test the start region iterator with nonnull cursor
+ */
+ @Test(groups = { "Functional" })
+ public void testBoundsIteratorUsingCursor()
+ {
+ List<int[]> hiddenColumns = new ArrayList<>();
+
+ // add some hidden columns
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ HiddenCursorPosition pos = new HiddenCursorPosition(0, 0);
+
+ Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
+ hiddenColumns);
+ assertTrue(it.hasNext());
+ Integer result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertFalse(it.hasNext());
+
+ it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(5, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertFalse(it.hasNext());
+
+ pos = new HiddenCursorPosition(1, 6);
+ hiddenColumns.add(new int[] { 47, 50 });
+
+ it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(19, (int) result);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(25, (int) result);
+ assertFalse(it.hasNext());
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class VisibleContigsIteratorTest
+{
+ /**
+ * Test the iterator with single visible regions
+ */
+ @Test(groups = { "Functional" })
+ public void testSimpleVisibleRegions()
+ {
+ List<int[]> hiddenColumns = null;
+
+ // null hidden columns
+ VisibleContigsIterator it = new VisibleContigsIterator(3, 10,
+ hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ int[] result = it.next();
+ assertEquals(3, result[0]);
+ assertEquals(9, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ hiddenColumns = new ArrayList<>();
+
+ // no hidden columns
+ it = new VisibleContigsIterator(3, 10,
+ hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(3, result[0]);
+ assertEquals(9, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ // hidden columns, but not where we are looking
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ it = new VisibleContigsIterator(2, 3, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(2, result[0]);
+ assertEquals(2, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(5, 7, hiddenColumns);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(11, 15, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(11, result[0]);
+ assertEquals(14, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(50, 60, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(50, result[0]);
+ assertEquals(59, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ }
+
+ /**
+ * Test the iterator with multiple visible regions
+ */
+ @Test(groups = { "Functional" })
+ public void testMultipleVisibleRegions()
+ {
+ List<int[]> hiddenColumns = new ArrayList<>();
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ // all hidden columns covered
+ VisibleContigsIterator it = new VisibleContigsIterator(3, 50,
+ hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ int[] result = it.next();
+ assertEquals(3, result[0]);
+ assertEquals(4, result[1]);
+
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(11, result[0]);
+ assertEquals(24, result[1]);
+
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(41, result[0]);
+ assertEquals(49, result[1]);
+
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ }
+
+ /**
+ * Test the iterator with regions which start/end at hidden region edges
+ */
+ @Test(groups = { "Functional" })
+ public void testVisibleRegionsAtHiddenEdges()
+ {
+ List<int[]> hiddenColumns = new ArrayList<>();
+ hiddenColumns.add(new int[] { 5, 10 });
+ hiddenColumns.add(new int[] { 25, 40 });
+
+ VisibleContigsIterator it = new VisibleContigsIterator(0, 10,
+ hiddenColumns);
+ assertTrue(it.hasNext());
+ assertTrue(it.endsAtHidden());
+ int[] result = it.next();
+ assertEquals(0, result[0]);
+ assertEquals(4, result[1]);
+ assertFalse(it.hasNext());
+ assertTrue(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(2, 11, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertTrue(it.endsAtHidden());
+ result = it.next();
+ assertEquals(2, result[0]);
+ assertEquals(4, result[1]);
+ assertFalse(it.hasNext());
+ assertTrue(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(2, 12, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(2, result[0]);
+ assertEquals(4, result[1]);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(11, result[0]);
+ assertEquals(11, result[1]);
+ assertFalse(it.hasNext());
+ assertFalse(it.endsAtHidden());
+
+ it = new VisibleContigsIterator(13, 25, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(13, result[0]);
+ assertEquals(24, result[1]);
+ assertFalse(it.hasNext());
+
+ it = new VisibleContigsIterator(13, 26, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertTrue(it.endsAtHidden());
+ result = it.next();
+ assertEquals(13, result[0]);
+ assertEquals(24, result[1]);
+ assertFalse(it.hasNext());
+
+ it = new VisibleContigsIterator(13, 27, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertTrue(it.endsAtHidden());
+ result = it.next();
+ assertEquals(13, result[0]);
+ assertEquals(24, result[1]);
+ assertFalse(it.hasNext());
+
+ it = new VisibleContigsIterator(13, 41, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertTrue(it.endsAtHidden());
+ result = it.next();
+ assertEquals(13, result[0]);
+ assertEquals(24, result[1]);
+ assertFalse(it.hasNext());
+
+ it = new VisibleContigsIterator(13, 42, hiddenColumns);
+ assertTrue(it.hasNext());
+ assertFalse(it.endsAtHidden());
+ result = it.next();
+ assertEquals(13, result[0]);
+ assertEquals(24, result[1]);
+ assertTrue(it.hasNext());
+ result = it.next();
+ assertEquals(41, result[0]);
+ assertEquals(41, result[1]);
+ }
+}
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@BeforeClass(alwaysRun = true)
public void setUp()
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
String chainACommand = commands[0].commands[0];
// M colour is #82827d == (130, 130, 125) (see strand.html help page)
assertTrue(chainACommand
- .contains(";select 21:A/1.1;color[130,130,125]"));
+ .contains("select 21:A/1.1;color[130,130,125]")); // first one
// H colour is #60609f == (96, 96, 159)
assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
// hidden columns are Gray (128, 128, 128)
String chainBCommand = commands[1].commands[0];
// M colour is #82827d == (130, 130, 125)
assertTrue(chainBCommand
- .contains(";select 21:B/2.1;color[130,130,125]"));
+ .contains("select 21:B/2.1;color[130,130,125]"));
// V colour is #ffff00 == (255, 255, 0)
assertTrue(chainBCommand
.contains(";select 22:B/2.1;color[255,255,0]"));
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
*/
assertFalse(alignFrame.hideFeatureColumns("exon", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy().isEmpty());
+
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
+
assertFalse(alignFrame.hideFeatureColumns("exon", false));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy().isEmpty());
+
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
/*
* hiding a feature in all columns does nothing
*/
assertFalse(alignFrame.hideFeatureColumns("Metal", true));
assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
- List<int[]> hidden = alignFrame.getViewport().getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy();
- assertTrue(hidden.isEmpty());
+
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 0);
+
/*
* threshold Metal to hide features where score < 5
fc.setThreshold(5f);
alignFrame.getFeatureRenderer().setColour("Metal", fc);
assertTrue(alignFrame.hideFeatureColumns("Metal", true));
- hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy();
- assertEquals(hidden.size(), 1);
- assertEquals(hidden.get(0)[0], 5);
- assertEquals(hidden.get(0)[1], 9);
+ HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+ assertEquals(hidden.getNumberOfRegions(), 1);
+ Iterator<int[]> regions = hidden.iterator();
+ int[] next = regions.next();
+ assertEquals(next[0], 5);
+ assertEquals(next[1], 9);
/*
* hide a feature present in some columns
*/
alignFrame.getViewport().showAllHiddenColumns();
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
- hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy();
- assertEquals(hidden.size(), 2);
- assertEquals(hidden.get(0)[0], 1);
- assertEquals(hidden.get(0)[1], 3);
- assertEquals(hidden.get(1)[0], 6);
- assertEquals(hidden.get(1)[1], 8);
+ regions = alignFrame.getViewport().getAlignment()
+ .getHiddenColumns().iterator();
+ assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .getNumberOfRegions(), 2);
+ next = regions.next();
+ assertEquals(next[0], 1);
+ assertEquals(next[1], 3);
+ next = regions.next();
+ assertEquals(next[0], 6);
+ assertEquals(next[1], 8);
}
@BeforeClass(alwaysRun = true)
@Test(groups = "Functional")
public void testChangeColour_background_groupsAndThresholds()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
@Test(groups = "Functional")
public void testColourThresholdActions()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
@Test(groups = "Functional")
public void testNewView_colourThresholds()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
*/
af.newView_actionPerformed(null);
assertEquals(af.alignPanel.getViewName(), "View 1");
- AlignViewport av2 = af.getViewport();
+ AlignmentViewport av2 = af.getViewport();
assertNotSame(av, av2);
assertSame(av2, af.alignPanel.av);
rs = av2.getResidueShading();
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import java.util.ArrayList;
AlignmentI al;
- AlignViewport testee;
+ AlignmentViewport testee;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
SequenceGroup sg1 = new SequenceGroup();
SequenceGroup sg2 = new SequenceGroup();
SequenceGroup sg3 = new SequenceGroup();
jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
- Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ AlignViewportI av = af.getViewport();
+ Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getOccupancyAnnotation(), "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
- null, av.getAlignmentGapAnnotation().label))
+ null, av.getOccupancyAnnotation().label))
{
c++;
}
String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
DataSourceType.PASTE);
- AlignViewport testme = af.getViewport();
+ AlignmentViewport testme = af.getViewport();
SequenceI cons = testme.getConsensusSeq();
assertEquals("A-C", cons.getSequenceAsString());
}
import jalview.io.FormatAdapter;
import java.io.IOException;
-import java.util.List;
+import java.util.Iterator;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
HiddenColumns currentHidden = af.getViewport().getAlignment()
.getHiddenColumns();
- List<int[]> regions = currentHidden.getHiddenColumnsCopy();
- assertEquals(regions.get(0)[0], 0);
- assertEquals(regions.get(0)[1], 3);
- assertEquals(regions.get(1)[0], 22);
- assertEquals(regions.get(1)[1], 25);
+ Iterator<int[]> regions = currentHidden.iterator();
+ int[] next = regions.next();
+ assertEquals(0, next[0]);
+ assertEquals(3, next[1]);
+ next = regions.next();
+ assertEquals(22, next[0]);
+ assertEquals(25, next[1]);
// now reset hidden columns
acc.reset();
currentHidden = af.getViewport().getAlignment().getHiddenColumns();
- regions = currentHidden.getHiddenColumnsCopy();
- assertEquals(regions.get(0)[0], 10);
- assertEquals(regions.get(0)[1], 20);
+ regions = currentHidden.iterator();
+ next = regions.next();
+ assertEquals(10, next[0]);
+ assertEquals(20, next[1]);
// check works with empty hidden columns as old columns
oldhidden = new HiddenColumns();
acc.reset();
currentHidden = af.getViewport().getAlignment().getHiddenColumns();
- regions = currentHidden.getHiddenColumnsCopy();
- assertEquals(regions.get(0)[0], 10);
- assertEquals(regions.get(0)[1], 20);
+ regions = currentHidden.iterator();
+ next = regions.next();
+ assertEquals(10, next[0]);
+ assertEquals(20, next[1]);
}
}
import static org.testng.Assert.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
import javax.swing.JTextArea;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class PairwiseAlignmentPanelTest
{
@Test(groups = "Functional")
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
AlignmentI al = viewport.getAlignment();
/*
String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Iterator;
import java.util.List;
import javax.swing.JMenu;
public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
{
JMenuItem menu = new JMenuItem();
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertFalse(menu.isEnabled());
// now try null list
List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
// create list of links and list of DBRefs
- List<String> links = new ArrayList<String>();
- List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+ List<String> links = new ArrayList<>();
+ List<DBRefEntry> refs = new ArrayList<>();
// links as might be added into Preferences | Connections dialog
links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
}
// if there are no valid links the Links submenu is disabled
- List<String> nomatchlinks = new ArrayList<String>();
+ List<String> nomatchlinks = new ArrayList<>();
nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
+ DB_ACCESSION + "$");
assertFalse(linkMenu.isEnabled());
}
+
+ /**
+ * Test for adding feature links
+ */
+ @Test(groups = { "Functional" })
+ public void testHideInsertions()
+ {
+ // get sequences from the alignment
+ List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+
+ // add our own seqs to avoid problems with changes to existing sequences
+ // (gap at end of sequences varies depending on how tests are run!)
+ Sequence seqGap1 = new Sequence("GappySeq",
+ "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
+ seqGap1.createDatasetSequence();
+ seqs.add(seqGap1);
+ Sequence seqGap2 = new Sequence("LessGappySeq",
+ "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
+ seqGap2.createDatasetSequence();
+ seqs.add(seqGap2);
+ Sequence seqGap3 = new Sequence("AnotherGapSeq",
+ "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
+ seqGap3.createDatasetSequence();
+ seqs.add(seqGap3);
+ Sequence seqGap4 = new Sequence("NoGaps",
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+ seqGap4.createDatasetSequence();
+ seqs.add(seqGap4);
+
+ ColumnSelection sel = new ColumnSelection();
+ parentPanel.av.getAlignment().getHiddenColumns()
+ .revealAllHiddenColumns(sel);
+
+ // get the Popup Menu for 7th sequence - no insertions
+ testee = new PopupMenu(parentPanel, seqs.get(7), null);
+ testee.hideInsertions_actionPerformed(null);
+
+ HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ Iterator<int[]> it = hidden.iterator();
+ assertFalse(it.hasNext());
+
+ // get the Popup Menu for GappySeq - this time we have insertions
+ testee = new PopupMenu(parentPanel, seqs.get(4), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ int[] region = it.next();
+ assertEquals(region[0], 4);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 10);
+ assertEquals(region[1], 10);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 18);
+ assertEquals(region[1], 20);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 24);
+ assertEquals(region[1], 34);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 45);
+ assertEquals(region[1], 46);
+
+ assertFalse(it.hasNext());
+
+ sel = new ColumnSelection();
+ hidden.revealAllHiddenColumns(sel);
+
+ // make a sequence group and hide insertions within the group
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(8);
+ sg.setEndRes(42);
+ sg.addSequence(seqGap2, false);
+ sg.addSequence(seqGap3, false);
+ parentPanel.av.setSelectionGroup(sg);
+
+ // hide columns outside and within selection
+ // only hidden columns outside the collection will be retained (unless also
+ // gaps in the selection)
+ hidden.hideColumns(1, 10);
+ hidden.hideColumns(31, 40);
+
+ // get the Popup Menu for LessGappySeq in the sequence group
+ testee = new PopupMenu(parentPanel, seqs.get(5), null);
+ testee.hideInsertions_actionPerformed(null);
+ hidden = parentPanel.av.getAlignment().getHiddenColumns();
+ it = hidden.iterator();
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 1);
+ assertEquals(region[1], 7);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 13);
+ assertEquals(region[1], 14);
+
+ assertTrue(it.hasNext());
+ region = it.next();
+ assertEquals(region[0], 34);
+ assertEquals(region[1], 34);
+ }
+
}
import static org.testng.Assert.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
public class SequenceRendererTest
{
AlignmentI al;
- AlignViewport av;
+ AlignViewportI av;
SequenceI seq1;
--- /dev/null
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.Option;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMERTest {
+
+ AlignFrame frame;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpBeforeClass() throws Exception
+ {
+ /*
+ * NB: check HMMER_PATH in testProps.jvprops is valid for
+ * the machine on which this runs
+ */
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/hmmer/testProps.jvprops", "-open",
+ "examples/uniref50.fa" });
+ frame = Desktop.getAlignFrames()[0];
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * Test with a dependency on locally installed hmmbuild binaries
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "External")
+ public void testHMMBuildThenHMMAlign()
+ throws MalformedURLException, IOException
+ {
+ /*
+ * run hmmbuild - note the side-effect of selecting the HMM
+ * sequence that gets added to the alignment
+ */
+ testHMMBuild();
+ HiddenMarkovModel hmm = frame.getSelectedHMM();
+ assertNotNull(hmm);
+
+ /*
+ * now run hmmalign - with respect to the select HMM profile
+ */
+ testHMMAlign();
+ }
+
+ public void testHMMBuild()
+ {
+ /*
+ * set up argument to run hmmbuild for the alignment
+ */
+ ArrayList<ArgumentI> params = new ArrayList<>();
+ String argName = MessageManager.getString("label.hmmbuild_for");
+ String argValue = MessageManager.getString("label.alignment");
+ params.add(
+ new Option(argName, null, false, null, argValue, null, null));
+
+ HMMBuild builder = new HMMBuild(frame, params);
+ builder.run();
+
+ SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+ HiddenMarkovModel hmm = seq.getHMM();
+ assertNotNull(hmm);
+
+ assertEquals(hmm.getLength(), 148);
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.getName(), "Alignment_HMM");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "0.648193");
+ }
+
+ public void testHMMAlign()
+ {
+ HMMAlign thread = new HMMAlign(frame,
+ new ArrayList<ArgumentI>());
+ thread.run();
+
+ AlignFrame[] alignFrames = Desktop.getAlignFrames();
+ if (alignFrames == null)
+ {
+ fail("No align frame loaded");
+ }
+
+ /*
+ * now have the original align frame, and another for realigned sequences
+ */
+ assertEquals(alignFrames.length, 2);
+ AlignmentI original = alignFrames[0].getViewport().getAlignment();
+ assertNotNull(original);
+ AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+ assertNotNull(realigned);
+ assertNotNull(original.getHmmConsensus());
+ assertNotNull(realigned.getHmmConsensus());
+
+ SequenceI ferCapan = original.findName("FER_CAPAN");
+ assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+ SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+ assertTrue(ferCapanRealigned.getSequenceAsString()
+ .startsWith("-------m-A----SVSAT"));
+ }
+}
+
--- /dev/null
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
+HMMER_PATH=/Users/gmcarstairs/software/hmmer-3.1b2-macosx-intel/binaries
import java.io.File;
import java.util.List;
+import org.junit.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void checkPDBannotationSource()
{
-
+ Assert.fail(
+ "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
for (SequenceI asq : al.getSequences())
{
for (AlignmentAnnotation aa : asq.getAnnotation())
{
System.out.println("CalcId: " + aa.getCalcId());
- if (StructureImportSettings.getDefaultPDBFileParser().equals(
- StructureParser.JALVIEW_PARSER))
+ if (StructureImportSettings.getDefaultPDBFileParser()
+ .equals(StructureParser.JALVIEW_PARSER))
{
assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @DataProvider(name = "initialAccessions")
+ static Object[][] getAccessions()
+ {
+ return new String[][] { { "UNIPROT", "P00338" },
+ { "UNIPROT", "Q8Z9G6" },
+ { "ENSEMBLGENOMES", "CAD01290" } };
+ }
+
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
*
* @throws Exception
*/
- @Test(groups = { "Operational" }, enabled = true)
- public void testRetrieveAndShowCrossref() throws Exception
+ @Test(
+ groups =
+ { "Operational" },
+ dataProvider = "initialAccessions",
+ enabled = true)
+ public void testRetrieveAndShowCrossref(String forSource,
+ String forAccession) throws Exception
{
List<String> failedDBRetr = new ArrayList<>();
List<String> keyseq = new ArrayList<>();
Map<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
- {
+// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+// {
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
int pass1 = 0, pass2 = 0, pass3 = 0;
// { pass 2 = 0 { pass 3 = 0 } }
do
{
- String first = did[0] + " " + did[1];
+ String first = forSource + " " + forAccession;//did[0] + " " + did[1];
AlignFrame af = null;
boolean dna;
AlignmentI retral;
// retrieve dbref
List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
- did[0], did[1]);
+ forSource, forAccession);
+ // did[0], did[1]);
if (afs.size() == 0)
{
failedDBRetr.add("Didn't retrieve " + first);
pass1++;
}
} while (pass1 < 3);
- }
+
if (failedXrefMenuItems.size() > 0)
{
for (String s : failedXrefMenuItems)
@Test(groups = "Functional")
public void testGetReadableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getReadableFormats().toString(), expected);
}
@Test(groups = "Functional")
public void testGetWritableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), expected);
- expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+ expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
assertEquals(formats.getWritableFormats(false).toString(), expected);
}
@Test(groups = "Functional")
public void testDeregisterFileFormat()
{
- String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+ String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
formats.deregisterFileFormat(FileFormat.Fasta.getName());
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
* re-register the format: it gets added to the end of the list
*/
formats.registerFileFormat(FileFormat.Fasta);
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, Fasta]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
}
{
try
{
- AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+ AlignmentI al;
+ if (format == FileFormat.HMMER3)
+ {
+ al = new FormatAdapter().readFile("examples/uniref50.hmm",
+ DataSourceType.FILE, FileFormat.HMMER3);
+ }
+ else
+ {
+ al = new FormatAdapter().readFile("examples/uniref50.fa",
DataSourceType.FILE, FileFormat.Fasta);
+ }
/*
* 'gap' is the gap character used in the alignment data file here,
AlignmentI reloaded = new FormatAdapter().readFile(formatted,
DataSourceType.PASTE, format);
List<SequenceI> reread = reloaded.getSequences();
- assertEquals("Wrong number of reloaded sequences", seqs.length,
- reread.size());
+ assertEquals("Wrong number of reloaded sequences", seqs.length,
+ reread.size());
+
int i = 0;
for (SequenceI seq : reread)
@DataProvider(name = "formats")
static Object[][] getFormats()
{
- List<FileFormatI> both = new ArrayList<FileFormatI>();
+ List<FileFormatI> both = new ArrayList<>();
for (FileFormatI format : FileFormats.getInstance().getFormats())
{
if (format.isReadable() && format.isWritable()
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMFileTest {
+
+ HMMFile fn3;
+
+ HMMFile pKinase;
+
+ HMMFile made1;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws IOException
+ {
+ fn3 = new HMMFile("test/jalview/io/test_fn3_hmm.txt",
+ DataSourceType.FILE);
+
+ pKinase = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ made1 = new HMMFile("test/jalview/io/test_MADE1_hmm.txt",
+ DataSourceType.FILE);
+ }
+
+ @Test(groups = "Functional")
+ public void testParse() throws IOException
+ {
+ HiddenMarkovModel hmm = pKinase.getHMM();
+ assertEquals(hmm.getName(), "Pkinase");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00069.17");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "Protein kinase domain");
+ assertEquals(hmm.getLength(), 260);
+ assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Thu Jun 16 11:44:06 2011");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "54");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "3.358521");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3106786190");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+ "70.30 70.30");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "70.30 70.30");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "70.20 70.20");
+
+ assertEquals(hmm.getSymbols(), "ACDEFGHIKLMNPQRSTVWY");
+
+ assertEquals(hmm.getMatchEmissionProbability(0, 'Y'), 0.16102, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(11, 'P'), 0.0130, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(24, 'I'), 0.02583, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(83, 'C'), 0.008549,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(332, 'E'), 0.07998,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(381, 'D'), 0.014465,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(475, 'Y'), 0.02213,
+ 0.001d);
+
+ assertEquals(hmm.getInsertEmissionProbability(1, 'C'), 0.012, 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(14, 'H'), 0.02411,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(23, 'L'), 0.06764,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(90, 'D'), 0.0623, 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(374, 'T'), 0.0623,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(470, 'P'), 0.0647,
+ 0.001d);
+
+ assertEquals(hmm.getStateTransitionProbability(2, 6), 0.3848, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(38, 3), 0.5382, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(305, 3), 0.2916, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(380, 0), 0.99, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(453, 1), 0.0066, 0.001d);
+
+ assertEquals(hmm.getNodeMapPosition(3), 3);
+ assertEquals(hmm.getReferenceAnnotation(7), '-');
+ assertEquals(hmm.getConsensusResidue(23), 't');
+ assertEquals(hmm.getMaskedValue(30), '-');
+ assertEquals(hmm.getConsensusStructure(56), 'S');
+
+ assertEquals(hmm.getNodeMapPosition(78), 136);
+ assertEquals(hmm.getReferenceAnnotation(93), '-');
+ assertEquals(hmm.getConsensusResidue(145), 'a');
+ assertEquals(hmm.getMaskedValue(183), '-');
+ assertEquals(hmm.getConsensusStructure(240), 'H');
+ }
+
+ /**
+ * Test that Jalview can parse an HMM file even with a bunch of 'mandatory'
+ * fields missing (including no MAP annotation or // terminator line)
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse_minimalFile() throws IOException
+ {
+ /*
+ * ALPH is absent, alphabet inferred from HMM header line
+ * Optional COMPO line is absent
+ * first line after HMM is a guide line for readability
+ * next line is BEGIN node insert emissions
+ * next line is BEGIN node transitions
+ * next line is first sequence node match emissions 1.1 1.2 1.3
+ * next line is first sequence node insert emissions 1.4 1.5 1.6
+ * last line is first sequence node transitions
+ */
+ //@formatter:off
+ String hmmData =
+ "HMMER3\n" +
+ "HMM P M J\n" +
+ // both spec and parser require a line after the HMM line
+ " m->m m->i m->d i->m i->i d->m d->d\n" +
+ " 0.1 0.2 0.3\n" +
+ " 0.4 0.5 0.6 0.7 0.8 0.9 0.95\n" +
+ " 1 1.1 1.2 1.3 - - - - -\n" +
+ " 1.4 1.5 1.6\n" +
+ " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n" +
+ " 2 1.01 1.02 1.03 - - - - -\n" +
+ " 1.04 1.05 1.06\n" +
+ " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n";
+ //@formatter:on
+ HMMFile parser = new HMMFile(hmmData, DataSourceType.PASTE);
+ HiddenMarkovModel hmm = parser.getHMM();
+ assertNotNull(hmm);
+ assertEquals(hmm.getSymbols(), "PMJ");
+ // no LENG property: this should return node count excluding BEGIN node
+ assertEquals(hmm.getLength(), 2);
+
+ // node 1 (implicitly mapped to column 0)
+ double prob = hmm.getMatchEmissionProbability(0, 'p');
+ assertEquals(prob, Math.pow(Math.E, -1.1));
+ prob = hmm.getInsertEmissionProbability(0, 'J');
+ assertEquals(prob, Math.pow(Math.E, -1.6));
+
+ // node 2 (implicitly mapped to column 1)
+ prob = hmm.getMatchEmissionProbability(1, 'M');
+ assertEquals(prob, Math.pow(Math.E, -1.02));
+ prob = hmm.getInsertEmissionProbability(1, 'm');
+ assertEquals(prob, Math.pow(Math.E, -1.05));
+ }
+
+ @Test(groups = "Functional")
+ public void testParseHeaderLines_amino() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_fn3_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ HMMFile testee = new HMMFile();
+ PA.setValue(testee, "hmm", hmm);
+ testee.parseHeaderLines(br);
+ br.close();
+ fr.close();
+
+ assertEquals(hmm.getName(), "fn3");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00041.13");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "Fibronectin type III domain");
+ assertEquals(hmm.getProperty(HMMFile.LENGTH), "86");
+ assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Fri Jun 20 08:22:31 2014");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "106");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "11.415833");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3564431818");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD), "8.00 7.20");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "8.00 7.20");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "7.90 7.90");
+ assertEquals(hmm.getViterbi(), "-9.7737 0.71847");
+ assertEquals(hmm.getMSV(), "-9.4043 0.71847");
+ assertEquals(hmm.getForward(), "-3.8341 0.71847");
+ }
+
+ @Test(groups = "Functional")
+ public void testParseHeaderLines_dna() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ HMMFile testee = new HMMFile();
+ PA.setValue(testee, "hmm", hmm);
+ testee.parseHeaderLines(br);
+ br.close();
+ fr.close();
+
+ assertEquals(hmm.getName(), "MADE1");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER),
+ "DF0000629.2");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon");
+ assertEquals(hmm.getProperty(HMMFile.LENGTH), "80");
+ assertEquals(hmm.getProperty(HMMFile.MAX_LENGTH), "426");
+ assertEquals(hmm.getAlphabetType(), "DNA");
+ assertTrue(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertFalse(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Tue Feb 19 20:33:41 2013");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "1997");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES), "3.911818");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3015610723");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+ "2.324 4.234");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "2.343 1.212");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "2.354 5.456");
+ assertEquals(hmm.getViterbi(), "-9.3632 0.71858");
+ assertEquals(hmm.getMSV(), "-8.5786 0.71858");
+ assertEquals(hmm.getForward(), "-3.4823 0.71858");
+ }
+
+ @Test(groups = "Functional")
+ public void testFillList() throws IOException
+ {
+ Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");
+ ArrayList<Double> filledArray = new ArrayList<>();
+
+ filledArray.add(0.27253);
+ filledArray.add(0.0907);
+ filledArray.add(0.00499);
+ filledArray.add(0.02024);
+ filledArray.add(0.00005);
+ filledArray.add(0.00909);
+ filledArray.add(0.01357);
+ filledArray.add(0.10026);
+ filledArray.add(0.001);
+
+ double[] testList = HMMFile.parseDoubles(scanner1, 9);
+
+ for (int i = 0; i < 9; i++)
+ {
+ assertEquals(testList[i], filledArray.get(i), 0.001d);
+ }
+
+ filledArray.clear();
+ scanner1.close();
+
+ Scanner scanner2 = new Scanner(
+ "1.346 5.554 35.345 5.64 1.4");
+ filledArray.add(0.2603);
+ filledArray.add(0.00387);
+ filledArray.add(0d);
+ filledArray.add(0.00355);
+ filledArray.add(0.2466);
+
+ testList = HMMFile.parseDoubles(scanner2, 5);
+
+ for (int i = 0; i < 5; i++)
+ {
+ assertEquals(testList[i], filledArray.get(i), 0.001d);
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testParseModel() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel testHMM = new HiddenMarkovModel();
+ String line = null;
+ do
+ {
+ line = br.readLine(); // skip header lines up to HMM plus one
+ } while (!line.startsWith("HMM "));
+ br.readLine();
+
+ made1.parseModel(br);
+ testHMM = made1.getHMM();
+
+ br.close();
+ fr.close();
+
+ assertEquals(testHMM.getMatchEmissionProbability(1, 'C'), 0.09267,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(25, 'G'), 0.07327,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(1092, 'C'), 0.04184,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(1107, 'G'), 0.07,
+ 0.001d);
+
+ assertEquals(testHMM.getInsertEmissionProbability(0, 'G'), 0.25,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(247, 'T'), 0.2776,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(1096, 'T'), 0.25,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(1111, 'T'), 0.25,
+ 0.001d);
+
+ assertEquals(testHMM.getStateTransitionProbability(1, 0), 0.9634,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(5, 1), 0.0203,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(14, 3), 0.2515,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(65, 4), 0.78808,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(1080, 2), 0.01845,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(1111, 6),
+ Double.NEGATIVE_INFINITY);
+ }
+
+ @Test(groups = "Functional")
+ public void testParseAnnotations()
+ {
+ HMMFile testFile = new HMMFile();
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ PA.setValue(testFile, "hmm", hmm);
+
+ List<HMMNode> nodes = new ArrayList<>();
+ nodes.add(new HMMNode()); // BEGIN node
+
+ hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+ hmm.setProperty(HMMFile.MAP, "yes");
+ hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+ hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "yes");
+ hmm.setProperty(HMMFile.MASKED_VALUE, "yes");
+ Scanner scanner = new Scanner("1345 t t t t");
+ HMMNode node = new HMMNode();
+ nodes.add(node);
+ testFile.parseAnnotations(scanner, node);
+
+ hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+ hmm.setProperty(HMMFile.MAP, "no");
+ hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+ hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "no");
+ hmm.setProperty(HMMFile.MASKED_VALUE, "no");
+ Scanner scanner2 = new Scanner("- y x - -");
+ node = new HMMNode();
+ nodes.add(node);
+ testFile.parseAnnotations(scanner2, node);
+
+ hmm.setNodes(nodes);
+
+ assertEquals(hmm.getNodeMapPosition(1), 1345);
+ assertEquals(hmm.getConsensusResidue(1), 't');
+ assertEquals(hmm.getReferenceAnnotation(1), 't');
+ assertEquals(hmm.getMaskedValue(1), 't');
+ assertEquals(hmm.getConsensusStructure(1), 't');
+
+ scanner.close();
+ }
+
+ /**
+ * tests to see if file produced by the output matches the file from the input
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testPrint_roundTrip() throws IOException
+ {
+ String output = pKinase.print();
+ HMMFile pKinaseClone = new HMMFile(
+ new FileParse(output, DataSourceType.PASTE));
+ HiddenMarkovModel pKinaseHMM = pKinase.getHMM();
+ HiddenMarkovModel pKinaseCloneHMM = pKinaseClone.getHMM();
+
+ checkModelsMatch(pKinaseHMM, pKinaseCloneHMM);
+ }
+
+ /**
+ * A helper method to check two HMM models have the same values
+ *
+ * @param model1
+ * @param model2
+ */
+ protected void checkModelsMatch(HiddenMarkovModel model1,
+ HiddenMarkovModel model2)
+ {
+ assertEquals(model1.getLength(), model2.getLength());
+
+ for (int i = 0; i < model1.getLength(); i++)
+ {
+ String msg = "For Node" + i;
+ assertEquals(model1.getNode(i).getMatchEmissions(),
+ model2.getNode(i).getMatchEmissions(), msg);
+ assertEquals(model1.getNode(i).getInsertEmissions(),
+ model2.getNode(i).getInsertEmissions(), msg);
+ assertEquals(model1.getNode(i).getStateTransitions(),
+ model2.getNode(i).getStateTransitions(), msg);
+
+ if (i > 0)
+ {
+ assertEquals(model1.getNodeMapPosition(i),
+ model2.getNodeMapPosition(i), msg);
+ assertEquals(model1.getReferenceAnnotation(i),
+ model2.getReferenceAnnotation(i), msg);
+ assertEquals(model1.getConsensusResidue(i),
+ model2.getConsensusResidue(i), msg);
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendProperties() throws FileNotFoundException
+ {
+ StringBuilder sb = new StringBuilder();
+ fn3.appendProperties(sb);
+
+ Scanner testScanner = new Scanner(sb.toString());
+
+ String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
+ "NAME fn3", "ACC PF00041.13",
+ "DESC Fibronectin type III domain", "LENG 86", "ALPH amino",
+ "RF no", "MM no", "CONS yes", "CS yes", "MAP yes",
+ "DATE Fri Jun 20 08:22:31 2014", "NSEQ 106", "EFFN 11.415833",
+ "CKSUM 3564431818", "GA 8.00 7.20", "TC 8.00 7.20",
+ "NC 7.90 7.90", "STATS LOCAL MSV -9.4043 0.71847",
+ "STATS LOCAL VITERBI -9.7737 0.71847",
+ "STATS LOCAL FORWARD -3.8341 0.71847" };
+
+ for (String value : expected)
+ {
+ assertEquals(testScanner.nextLine(), value);
+ }
+
+ testScanner.close();
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendModelAsString() throws FileNotFoundException
+ {
+ StringBuilder sb = new StringBuilder();
+ fn3.appendModelAsString(sb);
+ String string = sb.toString();
+
+ assertEquals(findValue(2, 2, 2, string), "4.42225");
+ assertEquals(findValue(12, 14, 1, string), "2.79307");
+ assertEquals(findValue(6, 24, 3, string), "0.48576");
+ assertEquals(findValue(19, 33, 2, string), "4.58477");
+ assertEquals(findValue(20, 64, 2, string), "3.61505");
+ assertEquals(findValue(3, 72, 3, string), "6.81068");
+ assertEquals(findValue(10, 80, 2, string), "2.69355");
+ assertEquals(findValue(16, 65, 1, string), "2.81003");
+ assertEquals(findValue(14, 3, 1, string), "2.69012");
+ assertEquals(findValue(11, 32, 1, string), "4.34805");
+ }
+
+ /**
+ * A helper method to find a token in the model string
+ *
+ * @param symbolIndex
+ * index of symbol being searched. First symbol has index 1.
+ * @param nodeIndex
+ * index of node being searched. Begin node has index 0. First node
+ * has index 1.
+ * @param line
+ * index of line being searched in node. First line has index 1.
+ * @param model
+ * string model being searched
+ * @return value at specified position
+ */
+ private String findValue(int symbolIndex, int nodeIndex, int line,
+ String model)
+ {
+ String value = "";
+ Scanner scanner = new Scanner(model);
+ scanner.nextLine();
+ scanner.nextLine();
+
+ for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
+ {
+ scanner.nextLine();
+ }
+ for (int node = 0; node < nodeIndex; node++)
+ {
+ scanner.nextLine();
+ scanner.nextLine();
+ scanner.nextLine();
+ }
+
+ for (int symbol = 0; symbol < symbolIndex; symbol++)
+ {
+ value = scanner.next();
+ if ("COMPO".equals(value))
+ {
+ scanner.next();
+ }
+ else if (value.length() < 7)
+ {
+ scanner.next();
+ }
+ }
+ scanner.close();
+ return value;
+ }
+}
+
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
TEST_SEQ_HEIGHT = expectedSeqs.size();
TEST_GRP_HEIGHT = expectedGrps.size();
TEST_ANOT_HEIGHT = expectedAnnots.size();
- TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopy().size();
+ TEST_CS_HEIGHT = expectedColSel.getNumberOfRegions();
exportSettings = new AlignExportSettingI()
{
{
HiddenColumns cs = testJsonFile.getHiddenColumns();
Assert.assertNotNull(cs);
- Assert.assertNotNull(cs.getHiddenColumnsCopy());
- List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
- Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
- Assert.assertEquals(hiddenCols.get(0), expectedColSel
- .getHiddenColumnsCopy().get(0),
+
+ Iterator<int[]> it = cs.iterator();
+ Iterator<int[]> colselit = expectedColSel.iterator();
+ Assert.assertTrue(it.hasNext());
+ Assert.assertEquals(cs.getNumberOfRegions(), TEST_CS_HEIGHT);
+ Assert.assertEquals(it.next(), colselit.next(),
"Mismatched hidden columns!");
}
+ actualGrp.getColourText());
System.out.println(expectedGrp.getDisplayBoxes() + " | "
+ actualGrp.getDisplayBoxes());
- System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
- + actualGrp.getIgnoreGapsConsensus());
+ System.out.println(expectedGrp.isIgnoreGapsConsensus() + " | "
+ + actualGrp.isIgnoreGapsConsensus());
System.out.println(expectedGrp.getSequences().size() + " | "
+ actualGrp.getSequences().size());
System.out.println(expectedGrp.getStartRes() + " | "
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
- && expectedGrp.getIgnoreGapsConsensus() == actualGrp
- .getIgnoreGapsConsensus()
+ && expectedGrp.isIgnoreGapsConsensus() == actualGrp
+ .isIgnoreGapsConsensus()
&& colourSchemeMatches
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
@BeforeTest(alwaysRun = true)
public static void clearDesktop()
{
- if (Desktop.instance != null && Desktop.getAlignFrames() != null)
+ if (Desktop.instance != null && Desktop.getFrames() != null
+ && Desktop.getFrames().length > 0)
{
Desktop.instance.closeAll_actionPerformed(null);
}
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.FeatureRenderer;
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import java.io.File;
+import java.io.IOException;
import java.util.Arrays;
import java.util.BitSet;
import java.util.HashMap;
// we might want to revise this in future
int aa_new_size = (aa_new == null ? 0 : aa_new.length);
int aa_original_size = (aa_original == null ? 0 : aa_original.length);
- Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
- Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+ Map<Integer, BitSet> orig_groups = new HashMap<>();
+ Map<Integer, BitSet> new_groups = new HashMap<>();
if (aa_new != null && aa_original != null)
{
testAlignmentEquivalence(al, newAl, true, true, true);
}
+
+ @Test(groups = { "Functional" })
+ public void testTypeToDescription()
+ {
+ assertEquals("Secondary Structure",
+ StockholmFile.typeToDescription("SS"));
+ assertEquals("Surface Accessibility",
+ StockholmFile.typeToDescription("SA"));
+ assertEquals("transmembrane", StockholmFile.typeToDescription("TM"));
+ assertEquals("Posterior Probability",
+ StockholmFile.typeToDescription("PP"));
+ assertEquals("ligand binding", StockholmFile.typeToDescription("LI"));
+ assertEquals("active site", StockholmFile.typeToDescription("AS"));
+ assertEquals("intron", StockholmFile.typeToDescription("IN"));
+ assertEquals("interacting residue",
+ StockholmFile.typeToDescription("IR"));
+ assertEquals("accession", StockholmFile.typeToDescription("AC"));
+ assertEquals("organism", StockholmFile.typeToDescription("OS"));
+ assertEquals("class", StockholmFile.typeToDescription("CL"));
+ assertEquals("description", StockholmFile.typeToDescription("DE"));
+ assertEquals("reference", StockholmFile.typeToDescription("DR"));
+ assertEquals("look", StockholmFile.typeToDescription("LO"));
+ assertEquals("Reference Positions",
+ StockholmFile.typeToDescription("RF"));
+
+ // case-sensitive:
+ assertEquals("Rf", StockholmFile.typeToDescription("Rf"));
+ assertEquals("junk", StockholmFile.typeToDescription("junk"));
+ assertEquals("", StockholmFile.typeToDescription(""));
+ assertNull(StockholmFile.typeToDescription(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testDescriptionToType()
+ {
+ assertEquals("SS",
+ StockholmFile.descriptionToType("Secondary Structure"));
+ assertEquals("SA",
+ StockholmFile.descriptionToType("Surface Accessibility"));
+ assertEquals("TM", StockholmFile.descriptionToType("transmembrane"));
+
+ // test is not case-sensitive:
+ assertEquals("SS",
+ StockholmFile.descriptionToType("secondary structure"));
+
+ // test is white-space sensitive:
+ assertNull(StockholmFile.descriptionToType("secondary structure "));
+
+ assertNull(StockholmFile.descriptionToType("any old junk"));
+ assertNull(StockholmFile.descriptionToType(""));
+ assertNull(StockholmFile.descriptionToType(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrint()
+ {
+ SequenceI seq1 = new Sequence("seq1", "LKMF-RS-Q");
+ SequenceI seq2 = new Sequence("seq2/10-15", "RRS-LIP-");
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2 };
+ AlignmentI al = new Alignment(seqs);
+
+ StockholmFile testee = new StockholmFile(al);
+
+ /*
+ * basic output (sequences only):
+ * sequence ids are padded with 9 spaces more than the widest id
+ */
+ String output = testee.print(seqs, true);
+ String expected = "# STOCKHOLM 1.0\n" + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n//\n";
+ assertEquals(expected, output);
+
+ /*
+ * add some dbrefs
+ */
+ seq1.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "P83527"));
+ seq2.addDBRef(new DBRefEntry("RFAM", "1", "AY119185.1"));
+ seq2.addDBRef(new DBRefEntry("EMBL", "1", "AF125575"));
+ output = testee.print(seqs, true);
+ // PFAM and RFAM dbrefs should be output as AC, others as DR
+ expected = "# STOCKHOLM 1.0\n" + "#=GS seq1/1-7 AC PF00111\n"
+ + "#=GS seq1/1-7 DR UNIPROT ; P83527\n"
+ + "#=GS seq2/10-15 AC AY119185.1\n"
+ + "#=GS seq2/10-15 DR EMBL ; AF125575\n"
+ + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n//\n";
+ assertEquals(expected, output);
+
+ /*
+ * add some sequence and alignment annotation
+ */
+ Annotation[] anns = new Annotation[5];
+ for (int i = 0; i < anns.length; i++)
+ {
+ anns[i] = new Annotation(String.valueOf((char) ('B' + i)),
+ "Desc " + i,
+ (char) ('C' + i), i + 3);
+ }
+
+ // expect "secondary structure" to be output as #=GR seqid SS
+ // using the secondary structure character (CDEFG) not display char (BCDEF)
+ AlignmentAnnotation aa1 = new AlignmentAnnotation("secondary structure",
+ "ssdesc", anns);
+ aa1.sequenceRef = seq1;
+ seq1.addAlignmentAnnotation(aa1);
+ al.addAnnotation(aa1);
+
+ // "sec structure" should not be output as no corresponding feature id
+ AlignmentAnnotation aa2 = new AlignmentAnnotation("sec structure",
+ "ssdesc", anns);
+ aa2.sequenceRef = seq2;
+ seq2.addAlignmentAnnotation(aa2);
+ al.addAnnotation(aa2);
+
+ // alignment annotation for Reference Positions: output as #=GC RF
+ AlignmentAnnotation aa3 = new AlignmentAnnotation("reference positions",
+ "refpos", anns);
+ al.addAnnotation(aa3);
+
+ // 'seq' annotation: output as seq_cons
+ AlignmentAnnotation aa4 = new AlignmentAnnotation("seq", "seqdesc",
+ anns);
+ al.addAnnotation(aa4);
+
+ // 'intron' annotation: output as IN_cons
+ AlignmentAnnotation aa5 = new AlignmentAnnotation("intron",
+ "introndesc", anns);
+ al.addAnnotation(aa5);
+
+ // 'binding site' annotation: output as binding_site
+ AlignmentAnnotation aa6 = new AlignmentAnnotation("binding site",
+ "bindingdesc", anns);
+ al.addAnnotation(aa6);
+
+ // 'autocalc' annotation should not be output
+ AlignmentAnnotation aa7 = new AlignmentAnnotation("Consensus",
+ "consensusdesc", anns);
+ aa7.autoCalculated = true;
+ al.addAnnotation(aa7);
+
+ // hidden annotation should not be output
+ AlignmentAnnotation aa8 = new AlignmentAnnotation("domains",
+ "domaindesc", anns);
+ aa8.visible = false;
+ al.addAnnotation(aa8);
+
+ output = testee.print(seqs, true);
+ //@formatter:off
+ expected =
+ "# STOCKHOLM 1.0\n"
+ + "#=GS seq1/1-7 AC PF00111\n"
+ + "#=GS seq1/1-7 DR UNIPROT ; P83527\n"
+ + "#=GS seq2/10-15 AC AY119185.1\n"
+ + "#=GS seq2/10-15 DR EMBL ; AF125575\n"
+ + "#=GR seq1/1-7 SS CDEFG\n"
+ + "seq1/1-7 LKMF-RS-Q\n"
+ + "seq2/10-15 RRS-LIP-\n"
+ + "#=GC RF BCDEF\n" + "#=GC seq_cons BCDEF\n"
+ + "#=GC IN_cons BCDEF\n" + "#=GC binding_site BCDEF\n"
+ + "//\n";
+ //@formatter:on
+ assertEquals(expected, output);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAnnotationCharacter()
+ {
+ SequenceI seq = new Sequence("seq", "abc--def-");
+
+ Annotation[] ann = new Annotation[8];
+ ann[1] = new Annotation("Z", "desc", 'E', 1f);
+ ann[2] = new Annotation("Q", "desc", ' ', 1f);
+ ann[4] = new Annotation("", "desc", 'E', 1f);
+ ann[6] = new Annotation("ZH", "desc", 'E', 1f);
+
+ /*
+ * null annotation in column (not Secondary Structure annotation)
+ * should answer sequence character, or '-' if null sequence
+ */
+ assertEquals('-',
+ StockholmFile.getAnnotationCharacter("RF", 0, ann[0], null));
+ assertEquals('d',
+ StockholmFile.getAnnotationCharacter("RF", 5, ann[5], seq));
+ assertEquals('-',
+ StockholmFile.getAnnotationCharacter("RF", 8, null, seq));
+
+ /*
+ * null annotation in column (SS annotation) should answer underscore
+ */
+ assertEquals('_',
+ StockholmFile.getAnnotationCharacter("SS", 0, ann[0], seq));
+
+ /*
+ * SS secondary structure symbol
+ */
+ assertEquals('E',
+ StockholmFile.getAnnotationCharacter("SS", 1, ann[1], seq));
+
+ /*
+ * no SS symbol, use label instead
+ */
+ assertEquals('Q',
+ StockholmFile.getAnnotationCharacter("SS", 2, ann[2], seq));
+
+ /*
+ * SS with 2 character label - second character overrides SS symbol
+ */
+ assertEquals('H',
+ StockholmFile.getAnnotationCharacter("SS", 6, ann[6], seq));
+
+ /*
+ * empty display character, not SS - answers '.'
+ */
+ assertEquals('.',
+ StockholmFile.getAnnotationCharacter("RF", 4, ann[4], seq));
+ }
+
+ /**
+ * Test to verify that gaps are input/output as underscore in STO annotation
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testRoundtripWithGaps() throws IOException
+ {
+ /*
+ * small extract from RF00031_folded.stk
+ */
+ // @formatter:off
+ String stoData =
+ "# STOCKHOLM 1.0\n" +
+ "#=GR B.taurus.4 SS .._((.))_\n" +
+ "B.taurus.4 AC.UGCGU.\n" +
+ "#=GR B.taurus.5 SS ..((_._))\n" +
+ "B.taurus.5 ACUU.G.CG\n" +
+ "//\n";
+ // @formatter:on
+ StockholmFile parser = new StockholmFile(stoData, DataSourceType.PASTE);
+ SequenceI[] seqs = parser.getSeqsAsArray();
+ assertEquals(2, seqs.length);
+
+ /*
+ * B.taurus.4 has a trailing gap
+ * rendered as underscore in Stockholm annotation
+ */
+ assertEquals("AC.UGCGU.", seqs[0].getSequenceAsString());
+ AlignmentAnnotation[] anns = seqs[0].getAnnotation();
+ assertEquals(1, anns.length);
+ AlignmentAnnotation taurus4SS = anns[0];
+ assertEquals(9, taurus4SS.annotations.length);
+ assertEquals(" .", taurus4SS.annotations[0].displayCharacter);
+ assertNull(taurus4SS.annotations[2]); // gapped position
+ assertNull(taurus4SS.annotations[8]); // gapped position
+ assertEquals('(', taurus4SS.annotations[3].secondaryStructure);
+ assertEquals("(", taurus4SS.annotations[3].displayCharacter);
+ assertEquals(')', taurus4SS.annotations[7].secondaryStructure);
+
+ /*
+ * output as Stockholm and verify it matches the original input
+ * (gaps output as underscore in annotation lines)
+ * note: roundtrip test works with the input lines ordered as above;
+ * can also parse in other orders, but then input doesn't match output
+ */
+ AlignmentFileWriterI afile = FileFormat.Stockholm
+ .getWriter(new Alignment(seqs));
+ String output = afile.print(seqs, false);
+ assertEquals(stoData, output);
+ }
}
--- /dev/null
+HMMER3/f [3.1 | February 2013]
+NAME MADE1
+ACC DF0000629.2
+DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+LENG 80
+MAXL 426
+ALPH DNA
+RF yes
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Tue Feb 19 20:33:41 2013
+NSEQ 1997
+EFFN 3.911818
+CKSUM 3015610723
+GA 2.324 4.234
+TC 2.343 1.212
+NC 2.354 5.456
+STATS LOCAL MSV -8.5786 0.71858
+STATS LOCAL VITERBI -9.3632 0.71858
+STATS LOCAL FORWARD -3.4823 0.71858
+HMM A C G T
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.24257 1.59430 1.62906 1.16413
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03960 3.94183 3.94183 1.46634 0.26236 0.00000 *
+ 1 2.69765 2.44396 2.81521 0.24089 1 t x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03960 3.94183 3.94183 1.46634 0.26236 1.09861 0.40547
+ 2 2.72939 2.37873 2.85832 0.24244 2 t x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03725 4.00179 4.00179 1.46634 0.26236 1.09861 0.40547
+ 3 0.16099 3.16370 2.87328 2.99734 3 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03604 4.03416 4.03416 1.46634 0.26236 1.09861 0.40547
+ 4 1.98862 2.42132 0.42649 2.10770 4 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03539 4.05203 4.05203 1.46634 0.26236 1.09861 0.40547
+ 5 1.96369 2.69532 0.36534 2.32099 5 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03764 4.06427 3.92372 1.46634 0.26236 1.09861 0.40547
+ 6 2.56994 2.11239 2.71946 0.30571 6 t x - -
+ 1.37159 1.41129 1.39124 1.37159
+ 0.03806 3.89715 4.07214 1.50442 0.25122 1.00714 0.45454
+ 7 2.58388 2.10353 2.64646 0.31253 12 t x - -
+ 1.38764 1.38524 1.38764 1.38465
+ 0.03494 4.03864 4.09125 1.40070 0.28293 1.09237 0.40860
+ 8 2.18552 2.70201 0.28821 2.64645 14 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03628 4.09157 3.96779 1.46634 0.26236 1.09861 0.40547
+ 9 2.16916 2.82142 0.28427 2.60854 15 g x - -
+ 1.38091 1.39033 1.38365 1.39033
+ 0.03566 4.00237 4.08886 1.38021 0.28972 1.01958 0.44745
+ 10 2.45517 2.15232 2.42886 0.34277 18 t x - -
+ 1.39065 1.39065 1.39065 1.37335
+ 0.03536 4.01212 4.09576 1.39554 0.28462 1.09775 0.40589
+ 11 2.10260 2.95484 0.28160 2.64222 21 g x - -
+ 1.36740 1.40555 1.40555 1.36740
+ 0.03843 3.92069 4.02468 1.44733 0.26814 1.09856 0.40549
+ 12 2.54740 0.30185 2.61355 2.21647 26 c x - -
+ 1.38748 1.38276 1.38748 1.38748
+ 0.03457 4.05446 4.09623 1.40847 0.28040 1.05496 0.42803
+ 13 0.28443 2.72003 2.32214 2.48149 28 a x - -
+ 1.38740 1.38740 1.38298 1.38740
+ 0.03441 4.05976 4.10001 1.41198 0.27926 1.09780 0.40587
+ 14 0.29412 2.55413 2.49679 2.35701 30 a x - -
+ 1.38194 1.39067 1.38194 1.39067
+ 0.03505 4.02482 4.10005 1.39522 0.28473 1.09929 0.40512
+ 15 0.18837 2.99710 2.82270 2.77556 33 a x - -
+ 1.39015 1.39472 1.37503 1.38539
+ 0.03725 3.97815 4.02618 1.37955 0.28994 1.10102 0.40426
+ 16 0.50816 2.05151 2.22111 1.82407 37 a x - -
+ 1.36727 1.38730 1.39683 1.39405
+ 0.04830 3.89881 3.61610 1.29026 0.32186 1.05306 0.42905
+ 17 2.11260 2.73141 0.29747 2.64152 41 g x - -
+ 1.36913 1.40376 1.40376 1.36913
+ 0.03705 3.93681 4.08299 1.44872 0.26771 1.07479 0.41759
+ 18 2.24459 1.90539 2.34054 0.43234 46 t x - -
+ 1.33632 1.42493 1.39937 1.38665
+ 0.04427 3.64574 4.06297 1.70501 0.20061 1.21309 0.35279
+ 19 0.44322 2.17202 2.18055 2.03175 57 a x - -
+ 1.41047 1.41471 1.36338 1.35797
+ 0.03970 3.81957 4.07540 1.65588 0.21186 1.22788 0.34660
+ 20 0.33340 2.42691 2.40824 2.25160 66 a x - -
+ 1.29389 1.44615 1.37917 1.43324
+ 0.04223 3.70146 4.09459 1.55158 0.23815 1.05880 0.42598
+ 21 2.50563 1.98543 2.69601 0.33746 74 t x - -
+ 1.39462 1.39462 1.42862 1.32990
+ 0.04184 3.80216 3.98177 1.80466 0.17976 1.00279 0.45705
+ 22 2.54484 1.97505 2.66483 0.33806 84 t x - -
+ 1.39134 1.39489 1.38662 1.37246
+ 0.03877 3.97504 3.95038 1.37620 0.29107 1.13932 0.38572
+ 23 2.10159 2.83856 0.29282 2.61635 88 g x - -
+ 1.39682 1.39682 1.35536 1.39682
+ 0.05046 3.75402 3.65808 1.08330 0.41321 1.13019 0.39004
+ 24 2.25298 0.61854 2.50691 1.29221 90 c x - -
+ 1.35803 1.49605 1.46737 1.24379
+ 0.06091 3.28322 3.83564 1.89752 0.16245 1.28788 0.32276
+ 25 1.27819 2.23285 0.76242 1.91259 106 g x - -
+ 1.29024 1.67349 1.68279 1.04597
+ 0.05752 3.44263 3.73311 2.58671 0.07825 1.26818 0.33037
+ 26 1.86925 2.58352 0.39466 2.33986 131 g x - -
+ 1.31084 1.49412 1.46666 1.29002
+ 0.04698 3.54257 4.07715 2.25245 0.11109 0.86163 0.54900
+ 27 2.38297 1.93394 2.39162 0.39800 151 t x - -
+ 1.33582 1.47359 1.44163 1.30411
+ 0.04951 3.48445 4.03783 2.15951 0.12260 1.21681 0.35122
+ 28 2.41717 2.17810 2.62774 0.32113 170 t x - -
+ 1.36805 1.48060 1.37439 1.32840
+ 0.04849 3.50958 4.05014 2.58370 0.07850 1.22399 0.34822
+ 29 2.57764 2.35132 2.56552 0.28512 194 t x - -
+ 1.43829 1.43458 1.24787 1.43829
+ 0.04667 3.56670 4.05428 2.49706 0.08591 1.23744 0.34267
+ 30 2.47248 2.07688 2.62257 0.33172 215 t x - -
+ 1.25120 1.52623 1.70635 1.15531
+ 0.08932 3.31524 3.01336 2.81842 0.06156 1.22909 0.34610
+ 31 2.25937 2.13157 2.02027 0.43957 248 t x - -
+ 1.18172 1.43522 1.72841 1.28150
+ 0.07936 2.93117 3.77395 2.46269 0.08906 0.60457 0.79034
+ 32 2.04508 2.84981 0.30490 2.58263 280 g x - -
+ 1.17665 1.66785 1.66218 1.16056
+ 0.05998 3.23615 3.96853 2.83684 0.06040 1.01952 0.44749
+ 33 2.45103 0.38098 2.56776 1.87147 317 c x - -
+ 1.24153 1.52524 1.60663 1.22783
+ 0.05538 3.39046 3.90294 2.73920 0.06680 1.18729 0.36391
+ 34 2.22082 0.36258 2.75077 2.02704 347 c x - -
+ 1.15008 1.62014 1.86511 1.10673
+ 0.06086 3.18178 4.04341 2.94504 0.05403 1.25991 0.33363
+ 35 0.27033 2.66664 2.52541 2.43767 388 a x - -
+ 1.24951 1.47565 1.41392 1.42074
+ 0.07123 3.00373 3.95552 3.13655 0.04440 1.28173 0.32512
+ 36 2.83107 2.41670 2.97197 0.22235 439 t x - -
+ 1.37071 1.57683 1.38637 1.23972
+ 0.05293 3.45216 3.91807 2.54402 0.08181 1.14651 0.38235
+ 37 2.52322 2.25084 2.45909 0.31611 465 t x - -
+ 1.26335 1.55077 1.59008 1.19965
+ 0.07504 3.13329 3.55006 3.08962 0.04659 1.13108 0.38962
+ 38 0.45807 2.30687 1.98940 2.03143 512 a x - -
+ 1.15472 1.67511 1.53797 1.26320
+ 0.09820 3.13076 2.99876 2.79197 0.06326 1.39915 0.28343
+ 39 2.37471 0.42180 2.44763 1.80427 550 c x - -
+ 1.23785 1.49058 1.48364 1.35502
+ 0.06081 3.19472 4.01643 2.41851 0.09327 0.94671 0.49105
+ 40 2.32826 1.95481 2.36781 0.40458 578 t x - -
+ 1.36586 1.46001 1.43000 1.29720
+ 0.05257 3.39673 4.03256 1.84862 0.17133 1.40979 0.27997
+ 41 2.68669 2.13935 2.81520 0.28200 592 t x - -
+ 1.34965 1.42793 1.45781 1.31633
+ 0.04735 3.57826 3.99988 2.09424 0.13144 1.22129 0.34934
+ 42 2.55904 2.16444 2.70859 0.29952 609 t x - -
+ 1.12072 1.61936 1.63578 1.26895
+ 0.07346 3.25910 3.42962 2.85641 0.05919 1.38363 0.28857
+ 43 1.99923 1.61027 2.26343 0.57851 646 t x - -
+ 1.32290 1.58747 1.61095 1.11018
+ 0.06656 3.08568 3.97944 2.44774 0.09046 0.75593 0.63407
+ 44 0.23887 2.79899 2.55209 2.60783 675 a x - -
+ 1.18557 1.50323 1.59070 1.31590
+ 0.05597 3.38637 3.88222 2.46900 0.08847 1.27945 0.32599
+ 45 0.29593 2.53488 2.53903 2.32335 701 a x - -
+ 1.08710 1.54222 1.59276 1.40430
+ 0.07539 2.94521 3.91062 1.91623 0.15918 1.22327 0.34852
+ 46 2.58352 2.40524 2.76700 0.25955 725 t x - -
+ 1.19685 1.58503 1.74852 1.14293
+ 0.06124 3.18279 4.02089 2.82961 0.06085 1.05474 0.42814
+ 47 2.13251 2.88788 0.29508 2.50964 764 g x - -
+ 1.20891 1.55463 1.68206 1.19000
+ 0.06526 3.12574 3.94910 2.41448 0.09367 1.10396 0.40280
+ 48 2.23841 2.99164 0.25118 2.72900 792 g x - -
+ 1.26330 1.55339 1.52606 1.24355
+ 0.05464 3.34968 4.01313 2.78872 0.06347 1.15133 0.38012
+ 49 2.57533 0.32900 2.64632 2.01501 824 c x - -
+ 1.35118 1.39828 1.40141 1.39516
+ 0.04340 3.79297 3.91506 1.59549 0.22666 1.20075 0.35806
+ 50 0.46433 2.04127 2.23437 2.00605 833 a x - -
+ 1.23062 1.36903 1.62282 1.36182
+ 0.05764 3.31530 3.92762 2.28791 0.10700 1.07910 0.41536
+ 51 0.27513 2.77017 2.28518 2.57549 853 a x - -
+ 1.27958 1.58726 1.46109 1.25394
+ 0.05750 3.30072 3.96214 2.60776 0.07656 1.25708 0.33475
+ 52 0.20149 2.86434 2.84551 2.69770 883 a x - -
+ 1.23645 1.62259 1.71174 1.10368
+ 0.05756 3.26729 4.02702 2.54508 0.08172 1.27391 0.32814
+ 53 0.26982 2.65833 2.50477 2.46835 911 a x - -
+ 1.36005 1.50358 1.48100 1.22550
+ 0.06921 3.37553 3.42118 2.36646 0.09851 1.27560 0.32748
+ 54 0.40022 2.19284 2.22687 2.20396 934 a x - -
+ 1.12070 1.60472 1.53213 1.35895
+ 0.05523 3.36752 3.94966 2.42917 0.09224 0.84774 0.55928
+ 55 2.11356 0.46400 2.46442 1.79955 960 c x - -
+ 1.23932 1.35913 1.50478 1.46331
+ 0.05187 3.47055 3.94022 2.35854 0.09933 1.12102 0.39445
+ 56 1.85868 0.79440 2.22069 1.25971 983 c x - -
+ 1.21951 1.50212 1.51138 1.34185
+ 0.06404 3.29054 3.69705 1.75742 0.18933 1.18410 0.36532
+ 57 1.33272 2.32720 0.71452 1.90215 999 g x - -
+ 1.12229 1.49343 1.56653 1.42255
+ 0.04920 3.46654 4.08749 2.17995 0.11996 1.31769 0.31164
+ 58 2.48337 0.43652 2.46331 1.68683 1017 c x - -
+ 1.34704 1.55461 1.38112 1.28222
+ 0.04823 3.61532 3.90311 2.20911 0.11631 1.00864 0.45368
+ 59 0.41659 2.44509 1.93972 2.20507 1034 a x - -
+ 1.38198 1.38198 1.39194 1.38932
+ 0.03641 3.98130 4.06929 1.35873 0.29704 1.31330 0.31325
+ 60 0.41612 2.39160 1.97116 2.21075 1037 a x - -
+ 1.03649 1.46430 1.57421 1.57557
+ 0.04769 3.52580 4.06641 2.32461 0.10294 0.84329 0.56263
+ 61 2.66264 2.12302 2.82746 0.28581 1056 t x - -
+ 1.36925 1.39635 1.38930 1.39048
+ 0.04097 3.97400 3.84718 1.39433 0.28502 1.12205 0.39395
+ 62 2.26510 2.13196 2.42551 0.37231 1060 t x - -
+ 1.37965 1.39147 1.39147 1.38264
+ 0.04082 3.91610 3.90805 1.24613 0.33914 0.95192 0.48776
+ 63 0.41244 2.25761 2.16787 2.12907 1062 a x - -
+ 1.34515 1.41203 1.41203 1.37753
+ 0.04054 3.77835 4.08203 1.30483 0.31638 1.11819 0.39582
+ 64 2.51464 0.37905 2.62296 1.82008 1068 c x - -
+ 1.39543 1.38753 1.39233 1.37008
+ 0.03854 3.90584 4.03535 1.36573 0.29463 1.13682 0.38689
+ 65 2.16380 2.11332 2.18714 0.42765 1073 t x - -
+ 1.38764 1.38471 1.38519 1.38764
+ 0.03575 4.05376 4.03073 1.40080 0.28289 1.03825 0.43707
+ 66 2.79349 2.39141 2.87271 0.23478 1075 t x - -
+ 1.37227 1.39101 1.39101 1.39101
+ 0.03597 4.01447 4.05827 1.39017 0.28639 1.06429 0.42308
+ 67 2.82488 2.47749 2.93179 0.21887 1078 t x - -
+ 1.38141 1.39112 1.38915 1.38353
+ 0.03661 3.99477 4.04370 1.35958 0.29675 1.13439 0.38804
+ 68 2.77679 2.30433 2.90694 0.24425 1081 t x - -
+ 1.37593 1.38989 1.45520 1.32825
+ 0.04447 3.68736 3.99242 1.76176 0.18843 0.98580 0.46703
+ 69 2.47698 3.17398 0.19595 2.95437 1093 g x - -
+ 1.38264 1.38264 1.39734 1.38264
+ 0.05358 3.96553 3.40487 1.40348 0.28202 1.03112 0.44100
+ 70 2.84327 0.27906 2.97336 2.00890 1097 c x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03412 4.08811 4.08811 1.46634 0.26236 0.69006 0.69625
+ 71 0.21870 2.83638 2.69251 2.65798 1098 a x - -
+ 1.37446 1.37942 1.39640 1.39509
+ 0.03670 3.93983 4.09935 1.41905 0.27700 1.10002 0.40476
+ 72 2.35233 0.46085 2.23804 1.78715 1103 c x - -
+ 1.38536 1.38781 1.38781 1.38421
+ 0.03493 4.03822 4.09272 1.39310 0.28542 1.09638 0.40658
+ 73 2.57111 0.32543 2.74124 1.98892 1105 c x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03381 4.09688 4.09688 1.46634 0.26236 1.09626 0.40664
+ 74 0.27014 2.61416 2.53262 2.47636 1106 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03461 4.09267 4.05587 1.46634 0.26236 1.09748 0.40603
+ 75 0.52873 2.16549 1.91736 1.90409 1107 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03426 4.08396 4.08396 1.46634 0.26236 1.07423 0.41788
+ 76 2.33134 0.38082 2.65861 1.90055 1108 c x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03466 4.07266 4.07266 1.46634 0.26236 1.09861 0.40547
+ 77 2.20588 0.45134 2.35553 1.84373 1109 c x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03550 4.04912 4.04912 1.46634 0.26236 1.09861 0.40547
+ 78 2.69018 2.22054 2.82311 0.26898 1110 t x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03711 4.00561 4.00561 1.46634 0.26236 1.09861 0.40547
+ 79 0.16248 3.15867 2.86159 2.98963 1111 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.04048 3.92018 3.92018 1.46634 0.26236 1.09861 0.40547
+ 80 0.17484 3.04770 2.86638 2.88183 1112 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02045 3.90014 * 1.46634 0.26236 0.00000 *
+//
--- /dev/null
+HMMER3/e [3.0 | March 2010]
+NAME Pkinase
+ACC PF00069.17
+DESC Protein kinase domain
+LENG 260
+ALPH amino
+RF no
+CONS yes
+CS yes
+MAP yes
+DATE Thu Jun 16 11:44:06 2011
+NSEQ 54
+EFFN 3.358521
+CKSUM 3106786190
+GA 70.30 70.30
+TC 70.30 70.30
+NC 70.20 70.20
+STATS LOCAL MSV -10.7215 0.70254
+STATS LOCAL VITERBI -11.6541 0.70254
+STATS LOCAL FORWARD -5.2305 0.70254
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.60017 4.19886 2.94089 2.63789 3.35087 2.89119 3.48337 2.79435 2.60265 2.43454 3.62613 3.06133 3.41286 3.09693 2.94507 2.65650 2.87761 2.67871 4.54052 3.43274
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.00000 *
+ 1 2.91704 4.31028 4.76351 3.63148 2.10912 3.47710 4.39734 2.27639 3.96619 1.99282 3.42844 4.19567 4.43771 4.11903 3.67403 3.22736 3.14918 2.35905 3.32515 1.82622 1 y - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 2 2.77204 4.20708 3.06476 1.97968 4.66603 3.66509 3.19858 3.37903 2.25347 3.34018 4.38833 2.97180 4.05804 2.36838 2.43173 2.67542 2.50268 2.83403 5.78758 4.38976 2 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 3 2.90076 4.04294 3.31590 2.80413 3.08157 3.87481 4.12616 2.18958 2.49735 1.97194 3.73714 3.32717 3.98753 3.23115 3.12315 2.99137 2.62008 2.29426 5.21478 3.75979 3 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 4 2.89383 4.85429 3.10311 2.63174 3.71383 2.56808 3.47232 2.82076 2.61844 1.98342 3.72320 3.05498 4.17347 3.05527 3.32194 2.85608 2.93671 2.18878 5.40057 3.87183 4 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 5 2.68261 5.39185 2.80437 1.87471 4.73638 2.79887 3.69591 4.22191 2.19487 3.69685 4.08896 3.12413 3.70490 2.48424 2.08916 2.53260 3.02309 3.43812 5.82480 4.41426 5 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 6 2.77253 4.06085 3.07881 2.53373 4.10647 3.71564 3.68370 2.64290 2.00036 2.72968 4.17370 3.24239 3.08607 2.77632 2.72820 2.69921 2.54335 2.71931 5.60386 4.26496 6 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 7 3.42930 4.74416 5.34765 4.76823 3.71832 4.71430 5.09461 1.33015 3.54417 1.12594 3.33523 4.84641 5.00427 4.73010 4.64986 4.05097 3.66327 1.83083 5.51142 4.37013 7 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 8 2.57460 4.94286 4.00732 3.93216 5.40516 0.41612 5.15134 4.86315 4.18766 4.52736 5.33508 4.05990 4.45245 3.74651 4.46171 3.15888 3.14590 4.15180 6.71159 5.52767 8 G - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 9 2.30218 5.38172 3.03799 2.02026 4.18991 3.65799 3.84554 3.67215 2.28945 3.68495 4.42365 2.84227 3.73039 2.44555 2.39428 2.00278 2.95859 3.63127 5.81726 4.40923 9 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 10 4.54226 6.07621 5.39207 5.44513 6.34643 0.07137 6.34600 6.33790 5.73770 5.76452 6.83374 5.56171 5.46536 5.98137 5.73783 4.76037 5.08470 5.67502 7.03864 6.52156 10 G - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 11 2.06444 5.37337 2.91595 2.40063 4.70969 2.61181 3.84889 4.18948 2.46835 3.67503 4.41668 2.62917 4.05392 2.88235 2.66711 2.00495 2.47288 3.39649 5.81159 4.40596 11 s - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 12 2.90920 4.46494 4.12493 3.14570 1.52027 3.22992 4.24969 2.92840 3.46467 2.66529 3.12827 3.55640 4.33979 3.72214 3.72236 2.53517 2.98442 2.55125 5.06498 2.30159 12 f - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 13 2.21104 4.80722 4.64199 4.55509 5.54982 0.52550 5.49025 5.04875 4.70671 4.72740 5.47955 4.30215 4.43233 4.84666 4.86038 1.95116 3.45005 4.17507 6.87595 5.79039 13 G - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 14 2.71551 3.46186 3.01248 2.27453 4.55840 3.55853 3.50842 3.55064 2.03335 3.34882 4.31847 3.17065 4.07218 2.83960 2.83653 2.25762 2.26864 2.61469 5.72841 4.35037 14 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 15 3.17885 3.97005 5.63014 5.16553 4.35293 4.89782 5.77682 2.09398 5.06494 2.94083 4.14496 5.20428 5.30924 5.30763 5.20260 4.32158 3.61414 0.44769 6.26043 5.04118 15 V - - E
+ 2.68625 4.42232 2.77526 2.73102 3.46361 2.40519 3.72501 3.29361 2.67747 2.69306 4.24696 2.90353 2.73746 3.18153 2.89807 2.37893 2.77526 2.98499 4.58484 3.61510
+ 0.09563 2.43065 5.73865 0.67073 0.71608 0.48576 0.95510
+ 16 2.91101 3.31342 4.36759 3.41772 2.45121 4.01227 4.31421 2.75922 2.81772 2.31733 3.50420 3.69862 4.38187 3.88257 3.14725 3.02772 3.14303 2.46483 3.37889 1.69905 18 y - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 17 2.88484 5.28431 3.03179 2.31849 4.58595 3.47769 3.54625 2.98124 1.69233 2.43413 4.04064 3.16353 4.06907 2.72555 2.58277 2.55274 3.04512 3.20501 5.74377 4.36100 19 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 18 1.57125 2.56460 3.38436 3.39201 3.66458 2.34190 4.20526 2.93932 3.32823 2.44127 3.26099 3.74334 4.30466 3.60817 3.63469 3.01628 2.92537 2.55308 5.13581 3.91882 20 a - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 19 2.89298 4.40558 3.44708 2.63051 3.77015 3.77747 2.87940 2.57515 2.33949 2.85128 3.20054 3.37379 4.16367 2.65910 2.52913 2.67954 2.59930 2.46709 5.42679 3.74337 21 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 20 2.88350 5.37811 2.42858 2.28192 4.71668 3.65945 2.35349 4.19788 2.20596 2.91798 4.42054 2.38258 4.05280 2.81490 2.60119 2.77457 3.11461 3.76528 3.43428 3.80493 22 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 21 2.59359 5.30144 3.00667 2.46268 4.60954 3.67285 3.22394 2.91749 2.13087 2.60378 4.35201 3.05590 3.51881 2.48537 2.35096 2.62551 3.00998 2.84793 5.75687 4.36947 23 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 22 2.64500 5.38003 2.46961 2.36386 4.71962 2.36153 3.71093 3.77963 2.19342 3.27291 4.42213 2.49968 3.44456 2.94396 2.94770 2.23767 2.90215 3.58800 5.81601 3.79868 24 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 23 2.71410 5.35453 2.26257 2.17828 4.68327 3.06138 3.85215 3.65600 2.51871 3.65284 4.39957 2.64619 4.05631 2.95399 2.98284 2.41102 1.94961 3.19379 5.79713 3.78693 25 t - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03260 5.01631 3.67114 0.61958 0.77255 0.48576 0.95510
+ 24 2.77509 4.50579 3.06414 2.40741 4.68877 2.10468 3.84020 4.16638 2.52713 3.65577 4.39945 2.31826 2.82304 2.55347 2.45557 2.51717 3.10489 3.55245 5.79545 3.68618 26 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.13496 4.99383 2.12471 0.61958 0.77255 0.54753 0.86365
+ 25 2.82390 4.23357 2.59579 2.09029 4.65095 3.47120 3.53571 3.50264 1.93281 3.24335 4.10745 2.98984 3.99409 2.41262 2.43858 2.60001 2.84781 3.57090 5.75206 3.98239 27 k - - E
+ 2.68634 4.42166 2.77510 2.73101 3.46370 2.40521 3.72473 3.29370 2.67713 2.69347 4.24706 2.90350 2.73742 3.18145 2.89817 2.37895 2.77536 2.98516 4.58493 3.61485
+ 0.21086 2.33296 2.37401 1.37928 0.29003 0.81455 0.58490
+ 26 2.79249 4.86773 3.27912 2.48247 3.81836 3.65430 3.86742 2.36980 2.31612 2.40000 3.66176 2.98804 3.52938 2.45192 2.80383 2.80149 2.71760 2.93241 5.39419 3.83742 36 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01259 4.77670 5.49905 0.61958 0.77255 0.27298 1.43175
+ 27 2.94684 4.40681 4.93000 4.33270 2.14562 4.19543 4.43742 2.60780 4.12995 2.51432 3.32273 4.32339 4.55150 4.25562 4.15094 3.50804 3.26683 1.12964 4.39266 2.23526 37 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 28 0.67405 4.13502 4.78133 4.26234 4.00859 4.13420 4.88775 2.58668 4.14876 2.87877 3.59530 4.37511 4.66004 4.38446 4.34251 3.50924 3.44597 2.20111 5.62436 4.43519 38 A - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 29 2.77559 4.05359 4.82280 4.21814 3.45081 3.88127 4.46447 1.69887 3.29990 2.06046 2.92956 4.25618 4.49083 4.18293 4.07725 3.28739 3.19210 1.31639 4.98894 3.80930 39 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 30 4.13385 6.06880 4.58555 3.84767 5.73274 4.53840 4.41573 5.06650 0.32256 4.37802 5.30885 4.14872 4.92009 3.55775 2.54913 4.11741 4.25754 4.75872 6.25921 5.22828 40 K - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 31 2.53136 3.93442 3.55191 2.54113 3.59001 3.81267 3.67691 2.09853 2.22431 2.85063 3.63116 3.45300 4.19661 2.87681 2.71089 2.96116 2.67441 2.46338 5.34241 3.76111 41 i - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 32 2.80227 4.30542 4.81704 3.71619 2.31247 3.45194 4.41496 1.85614 4.00698 1.68898 3.06826 4.22398 4.44809 4.15126 4.03957 3.11345 3.01936 1.82478 4.92889 3.75130 42 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 33 2.72320 4.19698 2.89173 2.30854 4.21536 3.66470 3.63903 3.54937 1.81020 3.33297 4.38970 2.50126 3.12497 2.85129 2.61476 2.47307 2.93549 3.43057 4.63863 3.86554 43 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 34 2.73748 5.16363 3.24304 2.62749 4.42406 3.39882 3.64889 3.08793 1.75481 2.64054 4.22767 2.81684 3.49630 2.92572 2.69253 2.71691 2.78362 2.91622 5.65055 3.09244 44 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 35 2.82342 4.21564 2.57688 2.18304 4.09635 3.66104 3.29269 4.17416 2.24176 3.24419 4.40775 3.13331 3.02670 2.66210 2.30119 2.38622 2.91913 2.84969 5.80393 4.13733 45 e - - H
+ 2.68618 4.42225 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73731 3.18147 2.89801 2.37887 2.77520 2.98519 4.58477 3.61503
+ 0.02362 3.90596 5.73865 0.48782 0.95182 0.48576 0.95510
+ 36 2.81479 5.38805 2.34307 2.08229 3.84722 3.00939 3.24618 4.21561 2.24819 3.24444 4.42924 2.80965 3.63231 2.74299 2.65208 2.41080 2.72103 3.26063 5.82196 4.16400 47 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 37 2.42659 5.32934 2.94543 1.98753 4.27035 3.66735 3.85733 2.97282 2.27697 3.20526 3.75542 2.69174 3.50027 2.79550 2.45131 2.66535 2.70832 3.28701 5.77800 4.07668 48 e - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 38 2.82479 5.36482 2.46403 2.36491 4.23121 3.19666 3.53460 3.47934 2.01766 2.87145 4.06028 2.53791 3.88358 2.73438 2.79605 2.39315 2.94316 3.30320 5.80464 3.67777 49 k - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 39 2.81259 3.82036 2.58997 2.16257 3.93187 3.50795 3.44913 3.32347 2.23760 3.42042 3.43188 3.03914 3.18139 2.98833 2.90722 1.97318 3.04237 3.44327 4.85883 4.01646 50 s - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04017 5.01631 3.41907 0.61958 0.77255 0.48576 0.95510
+ 40 2.75150 4.68420 2.78864 2.20581 3.96394 3.14028 3.85474 3.62649 2.17804 2.84544 3.93254 2.66146 3.79370 2.72658 2.87564 2.43841 2.71937 3.23202 3.36778 4.34996 51 k - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01020 4.98634 5.70869 0.61958 0.77255 0.56699 0.83755
+ 41 2.52028 4.29421 2.93844 2.26593 3.28616 3.42961 3.89113 3.40312 1.92589 2.89626 3.59280 3.04537 4.08209 2.42956 3.02333 2.89065 2.87512 2.78376 5.62895 3.97726 52 k - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.06456 4.98634 2.88790 0.61958 0.77255 0.56699 0.83755
+ 42 2.52102 4.66200 2.60886 2.12080 3.90563 3.43164 3.41299 3.76759 2.19798 2.95231 4.37667 2.71584 3.31098 2.66775 2.46389 2.65499 2.89357 3.57073 4.74853 4.36793 53 e - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.06881 4.93254 2.82535 0.61958 0.77255 0.69302 0.69327
+ 43 2.65676 5.27743 2.81592 2.16715 4.59834 3.44096 3.79920 2.82354 2.10889 3.57233 3.78816 2.93522 4.00237 2.20078 2.58862 2.72374 2.99283 3.18643 5.72482 3.30249 54 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04191 4.87514 3.39892 0.61958 0.77255 0.80592 0.59181
+ 44 2.46416 5.14935 3.14274 2.35064 4.42785 3.46788 3.62138 3.06885 2.39724 2.90472 4.00413 2.77252 4.01153 2.56699 2.69346 2.37713 2.33258 3.34725 5.62407 3.30627 55 t - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.15381 4.84499 2.00472 0.61958 0.77255 0.85820 0.55151
+ 45 2.15178 5.11690 2.80767 2.47016 4.06926 3.56450 3.25874 3.42510 2.38373 2.72748 4.17388 2.58132 3.95629 2.68997 2.59104 2.52019 2.89357 3.10461 5.58730 3.84420 56 a - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.06869 4.70471 2.85898 0.61958 0.77255 1.05523 0.42788
+ 46 2.33893 4.38200 3.78128 3.08857 2.87706 3.76539 4.03303 2.50172 2.82237 2.26545 3.48958 3.56901 4.14175 3.13269 2.43377 3.02211 2.55318 2.18677 4.40164 3.75633 57 v - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.07407 4.65033 2.78326 0.61958 0.77255 1.03937 0.43646
+ 47 2.66580 4.77769 3.25859 2.69691 3.69577 3.61140 3.56963 3.36841 2.45062 2.28390 3.86113 2.83101 3.99793 3.01640 2.00932 2.40384 2.97180 2.98514 3.81809 4.01106 58 r - - H
+ 2.68588 4.42292 2.77574 2.73101 3.46421 2.40561 3.72562 3.29362 2.67747 2.69305 4.24679 2.90348 2.73776 3.18179 2.89693 2.37874 2.77432 2.98554 4.58544 3.61510
+ 0.56084 0.85690 5.33966 1.67148 0.20822 0.22069 1.61932
+ 48 3.87852 6.35819 2.88185 0.33512 5.75300 3.98086 4.66680 5.41085 3.73193 4.87592 5.81368 3.19190 4.67406 3.86930 4.28895 3.74624 4.21685 4.94226 6.88673 5.40485 78 E - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 49 2.34469 4.06185 4.67394 3.74635 3.19070 3.72385 4.38165 1.69529 3.89930 1.68521 3.30505 3.88179 4.42519 3.50953 3.71087 3.12279 3.14596 1.99339 4.94125 3.41486 79 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 50 2.41611 3.92039 3.06862 2.24055 4.69692 3.38839 3.50460 4.17440 2.17094 3.43336 4.01855 2.84870 4.05421 2.22409 2.42800 2.49697 2.93959 3.48161 5.80403 3.10747 80 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 51 2.65097 4.31309 4.79937 4.19096 3.25102 4.08746 4.41763 1.57396 3.99634 1.77576 3.18772 3.58572 4.45127 4.14513 4.03729 2.91921 3.15786 1.73265 4.93848 3.33785 81 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 52 2.71474 4.35776 4.49839 3.90546 3.26558 3.60358 3.11363 2.58541 3.76519 1.24138 2.56017 3.78382 4.40165 3.77674 3.90460 2.91080 2.88501 2.43218 4.97232 3.44306 82 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 53 2.21717 5.37509 3.13954 2.36108 4.71254 3.44569 3.50643 4.19289 1.90576 2.89362 4.41783 2.84264 3.50886 2.51670 2.27883 2.73413 2.79427 3.37900 5.81221 4.40629 83 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 54 2.88332 4.76187 3.15794 2.34306 4.64959 3.18467 2.98724 4.11774 2.20976 2.84622 3.53657 2.69640 4.06011 2.81953 2.22587 2.26090 2.67755 3.39248 5.77872 3.89328 84 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 55 2.92075 3.71086 4.82119 4.21031 2.91851 4.08375 4.41406 2.48059 4.00923 1.14255 2.77088 4.22517 4.44739 4.15194 3.51737 2.79440 3.04088 2.14784 4.92583 3.58797 85 l - - H
+ 2.68619 4.42231 2.77526 2.73130 3.46360 2.40505 3.72501 3.29360 2.67737 2.69361 4.24696 2.90322 2.73746 3.18153 2.89797 2.37878 2.77526 2.98514 4.58483 3.61509
+ 0.21093 1.81438 3.60337 0.15203 1.95873 0.48576 0.95510
+ 56 2.87228 4.32697 2.43695 2.52023 4.72535 3.09966 3.42727 4.21076 2.24746 3.68599 4.14994 2.21640 3.70120 2.45856 2.42604 2.20075 2.84715 3.77128 5.81417 4.40372 87 s - - S
+ 2.68626 4.42233 2.77498 2.73131 3.46362 2.40515 3.72479 3.29362 2.67733 2.69363 4.24698 2.90355 2.73719 3.18141 2.89809 2.37895 2.77498 2.98527 4.58485 3.61511
+ 0.08622 2.53438 5.71435 0.90816 0.51628 0.44628 1.02166
+ 57 2.95437 4.05540 4.02453 3.66262 4.73022 3.00582 0.63840 4.27369 3.61156 3.92435 4.76053 3.90244 4.38221 3.97389 3.93213 2.36608 3.39859 3.79517 6.08861 4.80370 91 H - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 58 2.74925 4.59154 2.64384 2.02057 4.69046 3.19970 3.85151 4.16644 2.39568 3.65893 3.99620 3.06676 1.73396 2.95270 2.98758 2.52836 2.96698 3.57815 5.80119 4.39902 92 p - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 59 2.77600 3.63123 3.60742 3.04389 2.88763 3.83093 3.22852 3.27052 2.82124 2.96220 3.83761 1.44485 4.21384 3.33393 3.26463 3.06163 2.84916 2.86372 5.30436 2.85576 93 n - - S
+ 2.68619 4.42226 2.77521 2.73125 3.46355 2.40506 3.72496 3.29355 2.67742 2.69356 4.24691 2.90348 2.73741 3.18148 2.89802 2.37880 2.77521 2.98520 4.58478 3.61504
+ 0.02736 3.73933 5.73865 0.64347 0.74542 0.48576 0.95510
+ 60 3.43736 4.73250 5.40681 4.85032 3.21534 3.89737 5.21348 0.72821 4.70181 2.29095 3.77438 4.92025 5.08011 4.86610 4.77171 4.12622 3.68020 1.72131 5.65218 4.46593 96 i - - B
+ 2.68620 4.42119 2.77522 2.73126 3.46356 2.40515 3.72497 3.29356 2.67743 2.69357 4.24692 2.90349 2.73742 3.18149 2.89780 2.37889 2.77522 2.98521 4.58479 3.61505
+ 0.04171 3.27988 5.73865 0.65380 0.73410 0.48576 0.95510
+ 61 3.22247 3.52386 5.20134 4.62057 3.74032 4.49428 4.89197 1.38422 4.44333 2.03444 3.40884 4.64781 4.83078 4.60265 4.48778 3.55308 3.01459 1.16992 5.37248 4.18666 99 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 62 2.72238 4.59459 3.13585 2.30027 4.72566 3.17722 3.67251 4.20868 2.00822 3.53187 4.42604 2.97500 3.44674 2.41134 2.06447 2.53711 2.32763 3.77297 5.81907 4.41084 100 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 63 2.75790 4.02501 4.89076 4.27684 2.25991 4.10991 4.44304 2.31340 4.06541 1.38378 2.56521 4.26823 4.47075 4.19670 4.07763 3.42134 2.72551 2.21249 4.93572 3.01728 101 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 64 2.79378 4.36122 4.48297 3.70404 2.84684 4.03133 3.55103 1.94759 2.82835 1.82248 3.32801 4.05424 4.39941 3.70850 3.13439 3.15759 3.14407 2.41334 4.25902 2.30786 102 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 65 2.47264 4.33075 2.07830 2.03157 4.71750 2.27093 3.18950 4.19892 2.58523 3.68152 4.42156 3.04070 4.05295 2.84140 2.67254 2.59104 3.11515 3.76615 5.81569 3.60292 103 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 66 2.10377 4.03530 4.82986 4.21790 2.76136 4.07923 4.41023 2.08081 4.01359 2.30827 2.78821 4.22543 4.44340 4.15406 4.03913 2.38166 2.60707 1.97272 3.19782 3.33258 104 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 67 2.82605 3.67894 3.38070 3.01266 1.82001 3.97118 3.82789 2.76491 3.48734 2.34143 3.24926 3.10725 3.78017 3.42990 3.73647 2.98277 3.13977 2.32864 3.87637 2.72935 105 f - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04987 5.01631 3.16967 0.61958 0.77255 0.48576 0.95510
+ 68 2.55964 4.21441 3.10666 1.94329 4.49707 3.21758 3.46239 3.37098 2.39709 3.00488 3.51821 3.06808 4.06187 2.54621 2.66989 2.75991 2.68522 3.13970 5.68635 3.14043 106 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02094 4.97674 4.28127 0.61958 0.77255 0.42506 1.06054
+ 69 2.80310 5.38415 2.22807 2.18295 4.72718 3.65266 3.36574 4.21171 2.46641 3.56699 4.42536 2.57848 3.46451 2.86899 2.36310 2.58224 2.17995 3.52075 5.81804 3.65548 107 t - - E
+ 2.68640 4.42162 2.77535 2.73147 3.46354 2.40551 3.72458 3.29233 2.67716 2.69348 4.24762 2.90375 2.73699 3.18187 2.89837 2.37858 2.77480 2.98522 4.58549 3.61548
+ 0.36809 1.18844 5.72853 1.68950 0.20409 0.46837 0.98355
+ 70 2.88244 5.39287 2.47300 2.29715 3.79460 2.82884 3.28660 4.22374 2.09832 3.69810 4.43357 2.45444 3.07035 2.85151 2.47539 2.34133 3.01376 3.78345 5.82560 4.10620 126 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 71 2.57798 5.39101 2.06614 2.42374 4.73510 2.82383 3.84381 4.22040 2.28304 3.69587 4.43195 2.62257 3.38372 2.71683 2.73886 2.29050 2.66881 3.34289 5.82427 4.18691 127 d - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 72 2.58231 5.35788 2.77781 2.22432 4.08337 3.66211 2.49021 4.16401 2.37240 3.16748 4.40241 2.52484 4.05523 2.76334 2.63486 2.49164 2.89823 3.30761 4.95167 3.05734 128 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 73 2.78575 3.74303 4.78141 4.17260 2.95491 4.07322 4.40160 1.89067 3.97854 1.60353 2.95383 3.71592 3.11906 4.12798 3.50390 3.07790 2.85145 2.24111 4.92509 2.91282 129 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 74 2.58399 2.76389 4.59675 3.99881 3.19843 4.04871 3.62339 2.65148 3.84111 2.12752 3.45456 3.62454 3.46238 4.02369 3.94739 2.79096 3.14543 2.42948 3.13888 1.74690 130 y - - E
+ 2.68624 4.42096 2.77500 2.73129 3.46360 2.40508 3.72501 3.29360 2.67747 2.69353 4.24696 2.90343 2.73746 3.18153 2.89807 2.37893 2.77510 2.98525 4.58483 3.61509
+ 0.10354 2.49668 4.13492 0.66960 0.71726 0.48576 0.95510
+ 75 3.07392 4.44555 4.97084 3.81418 2.87255 4.25097 4.57886 1.74564 4.16653 1.31678 2.12605 4.39109 4.59167 3.71495 4.19337 3.56380 3.30386 2.29390 5.05348 3.89648 133 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.52175 0.90012
+ 76 2.86449 3.41378 5.01300 4.41506 3.07458 4.28568 4.64425 1.49634 4.22335 2.27773 3.54368 4.43380 4.63588 3.70581 4.25773 3.60458 3.30826 1.19505 5.13861 3.95920 134 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.46390 0.99109
+ 77 2.91733 4.35063 4.55668 3.96112 2.40516 4.04680 4.36140 2.56068 3.81048 1.70108 1.79340 3.59899 4.41359 3.09405 3.93172 3.15547 2.48177 2.59902 4.96582 3.78095 135 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 78 2.76564 5.57030 2.50020 1.03018 4.90220 3.70297 3.44513 4.39514 2.75995 3.87044 4.62325 3.16505 3.19754 2.75935 3.27129 2.65802 3.28146 3.95557 6.00401 4.57374 136 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 79 2.81579 3.90369 4.68991 4.08721 2.27644 4.06399 3.63829 2.69790 3.58050 1.84024 3.31248 4.16081 4.42953 4.07816 3.60709 3.36667 3.01039 2.57256 4.40465 1.54393 137 y - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 80 2.45920 2.17262 4.69646 4.09287 3.22405 3.32199 3.21264 2.59887 3.91610 2.06244 2.25581 4.16309 3.61702 4.08102 3.98811 3.14866 3.14614 2.03766 4.93767 3.46778 138 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04171 5.01631 3.37486 0.61958 0.77255 0.48576 0.95510
+ 81 2.70314 5.37371 2.37994 1.91497 4.71601 2.93053 3.83161 4.20005 2.46492 3.55263 3.57885 2.58870 2.59223 2.74552 2.71928 2.69862 3.03649 3.29150 5.80804 4.39872 139 e - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01022 4.98481 5.70716 0.61958 0.77255 0.57090 0.83245
+ 82 2.41993 3.72287 3.12898 2.52046 4.44831 1.89639 3.49536 3.62837 2.38762 3.31281 3.53904 2.44913 3.42379 3.00780 3.12891 2.87912 2.75467 3.52812 5.65946 3.81984 140 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.10979 4.98481 2.33166 0.61958 0.77255 0.57090 0.83245
+ 83 2.77350 5.21303 2.43943 2.62703 4.54309 1.39496 3.89257 3.99092 2.60267 3.54085 4.32260 3.04209 4.06226 3.01831 3.03242 2.64588 2.77651 3.04353 5.73236 4.35922 141 g - - -
+ 2.68631 4.42210 2.77537 2.73126 3.46359 2.40522 3.72475 3.29338 2.67758 2.69250 4.24657 2.90377 2.73770 3.18148 2.89796 2.37902 2.77541 2.98478 4.58507 3.61496
+ 0.21230 1.67338 5.60865 1.39945 0.28334 0.33567 1.25476
+ 84 2.88583 5.39491 1.79381 2.06461 4.73890 3.24821 3.51210 4.22442 2.47141 3.51906 4.43601 2.95989 3.57031 2.79057 2.82788 2.02605 2.91163 3.62254 5.82805 4.41723 147 d - - B
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 85 2.90986 4.42406 3.70533 3.66371 3.02577 3.99009 3.90749 2.78363 3.56278 1.02082 3.24022 3.34355 4.36146 3.52102 3.78389 3.13807 2.95820 2.60948 5.03043 3.48016 148 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 86 2.57337 4.10245 3.03950 2.95233 2.09915 3.53742 3.15959 3.37138 2.66519 2.44003 3.54971 3.10382 3.71714 3.06888 3.13958 2.44794 3.05039 3.11306 4.61969 3.07664 149 f - - H
+ 2.68621 4.42228 2.77522 2.73126 3.46357 2.40516 3.72497 3.29357 2.67744 2.69358 4.24693 2.90350 2.73735 3.18149 2.89804 2.37890 2.77502 2.98521 4.58480 3.61458
+ 0.24291 3.02648 1.78874 0.58545 0.81386 0.48576 0.95510
+ 87 2.29362 5.30873 1.92419 2.32474 4.26868 3.43187 3.46788 4.12970 2.37357 3.61146 4.35100 2.92576 3.98105 2.69850 2.60197 2.47206 2.54407 3.69618 5.74493 3.96335 152 d - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01185 4.83724 5.55959 0.61958 0.77255 0.87096 0.54223
+ 88 2.24696 4.24235 4.56569 3.96478 2.41045 3.97137 3.29432 2.27668 3.43922 2.04964 3.19406 4.05576 4.33743 3.97000 3.38896 3.27217 3.06100 2.23241 4.18296 2.20711 153 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01185 4.83724 5.55959 0.61958 0.77255 0.87096 0.54223
+ 89 3.80243 5.01974 5.81731 5.27268 3.70245 5.26548 5.70409 1.30084 5.15744 0.98923 3.04180 5.42350 5.39649 5.16571 5.17462 4.65797 4.03105 1.75151 5.84473 4.80632 154 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01185 4.83724 5.55959 0.61958 0.77255 0.62617 0.76494
+ 90 2.48275 5.13868 3.18520 2.44727 3.97540 3.65122 3.65677 3.36126 2.16734 3.30486 3.19390 3.06911 4.04233 2.41632 2.75033 2.25069 2.41675 3.09873 5.62108 3.69504 155 k - - H
+ 2.68595 4.42186 2.77509 2.73103 3.46377 2.40517 3.72421 3.29387 2.67761 2.69368 4.24695 2.90368 2.73754 3.18175 2.89730 2.37895 2.77536 2.98514 4.58473 3.61505
+ 0.63487 1.25520 1.68753 1.39580 0.28453 0.74756 0.64154
+ 91 2.43987 5.24839 2.75312 2.20207 4.11839 3.54175 3.72993 4.06095 2.07671 3.34429 3.98666 2.75679 3.72576 2.60349 2.28520 2.46158 2.79062 3.43756 5.68761 3.81452 172 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01352 4.70589 5.42824 0.61958 0.77255 0.34096 1.24163
+ 92 2.56414 5.37054 2.84426 2.11401 4.71382 2.70860 2.88683 4.19851 2.19051 3.14492 4.41168 2.55924 4.03189 2.79129 2.63798 2.35762 3.09530 3.76022 5.80426 3.44686 173 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01035 4.97167 5.69402 0.61958 0.77255 0.60365 0.79145
+ 93 2.86527 4.78061 2.95620 2.59670 4.27271 1.99448 3.84571 3.48713 2.08881 3.39073 4.33266 2.46895 3.64059 2.84730 2.63768 2.84659 2.50396 3.24160 5.73764 4.35043 174 g - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01035 4.97167 5.69402 0.61958 0.77255 0.46145 0.99524
+ 94 2.57883 3.45102 3.31966 2.70191 4.02973 3.16828 3.76144 3.12068 2.26544 3.06289 4.10647 2.81108 2.70638 2.99156 2.57108 2.49596 2.68439 2.78596 4.48656 4.03099 175 k - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01001 5.00539 5.72774 0.61958 0.77255 0.51640 0.90799
+ 95 3.00846 4.37852 4.95050 4.33851 2.03946 4.18408 4.51243 2.07907 4.13124 1.32746 2.71567 3.86888 4.53472 4.25457 4.14405 3.49709 3.23945 2.15194 4.98866 3.35208 176 l - - T
+ 2.68632 4.42239 2.77534 2.73137 3.46298 2.40515 3.72509 3.29351 2.67755 2.69332 4.24641 2.90361 2.73734 3.18136 2.89815 2.37881 2.77519 2.98532 4.58491 3.61446
+ 0.13280 2.11108 5.72774 1.00017 0.45858 0.46707 0.98573
+ 96 2.55096 5.39506 2.51329 2.14467 4.73966 3.20813 3.84532 4.22553 2.37049 3.70015 4.43599 2.79265 3.16832 2.74582 2.82569 1.88822 2.42672 3.78548 5.82793 4.41687 180 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 97 2.55253 5.00371 2.91674 1.56530 3.77486 3.74196 3.71669 3.18678 2.77868 2.90828 3.00031 3.29724 3.28640 3.12328 3.07027 2.76413 2.89289 3.32236 3.74938 3.48354 181 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 98 2.59075 4.32000 2.44335 2.15201 3.95693 3.12347 3.34011 3.83572 2.30797 3.16698 3.93315 2.75363 3.60071 2.81660 2.61665 2.70578 2.85000 3.34465 3.67935 4.00275 182 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 99 2.65092 5.35978 2.44414 1.82235 4.69093 3.44711 3.03513 3.63938 2.46445 2.69072 4.40412 3.13476 3.87902 2.43027 2.99516 2.67955 2.75495 3.20344 5.80088 4.03299 183 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 100 1.86496 3.02665 4.71869 4.11439 3.41506 3.78632 4.39467 1.72869 3.93413 2.03606 3.25110 4.17623 4.43415 4.09606 3.42450 3.02051 2.94480 2.04904 4.94015 3.76003 184 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 101 2.66380 3.60669 3.09016 2.70629 3.97052 3.12773 3.91117 3.25572 1.80561 2.74214 4.19581 3.23071 4.10037 2.51557 2.19861 2.73033 3.11863 2.97558 5.62300 4.27841 185 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 102 2.65525 3.61780 2.73206 2.59880 2.91626 3.69337 3.17740 3.91061 2.06495 2.87551 3.62080 2.65252 4.08468 3.01717 2.55140 2.50072 2.84956 3.37543 5.67937 3.86408 186 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 103 2.78549 3.75825 4.89230 4.27707 2.37628 4.09576 4.42870 1.58181 4.06146 2.16353 2.83229 4.25917 4.45832 4.19107 4.06819 3.40747 3.15724 2.08428 3.94244 2.32199 187 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 104 1.91854 4.04767 4.83572 4.22341 2.21465 3.82491 4.41156 2.18264 4.01792 2.17430 2.43077 4.22827 4.44431 4.15736 4.04152 2.82624 2.88622 2.07903 4.25105 3.74133 188 a - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 105 2.59846 4.94560 3.39451 2.56515 3.67443 3.44440 3.79808 3.54150 2.22767 2.11264 4.02778 3.19297 4.14629 3.16161 2.51054 2.63727 2.68778 3.11215 4.13689 2.62651 189 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 106 2.71202 4.65478 2.93025 2.07602 4.70407 3.24619 3.70431 4.18261 2.58938 3.67040 4.10390 3.00747 4.05496 1.41184 3.00214 2.55548 2.74962 3.75459 5.80879 4.40428 190 q - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 107 3.40758 4.70636 5.39472 4.82751 3.82844 4.73217 5.15283 1.33187 4.66862 1.85779 2.55181 4.88258 5.03394 4.81634 4.72035 4.07618 2.46891 1.37416 5.58393 4.41648 191 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 108 2.29107 3.23763 4.81578 4.20571 3.00975 3.26830 4.41487 2.37700 4.00619 1.39060 3.28560 4.22330 4.44775 4.15070 4.03923 2.94875 3.15303 1.86969 4.92930 3.75166 192 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 109 2.62933 4.07203 2.95927 2.08969 4.71415 3.53463 3.84677 3.97436 2.17805 2.82549 4.41873 2.79932 4.05232 2.53645 2.16719 2.25459 2.86145 3.76301 5.81311 4.40656 193 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 110 1.17650 4.82606 4.24050 3.83461 4.98724 1.08848 4.85992 4.42183 3.81285 4.07900 4.88120 3.97861 4.34888 4.10941 3.49121 2.50205 3.18154 3.58125 6.30917 5.10145 194 g - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 111 3.90271 5.14012 5.90469 5.33230 3.41122 5.28833 5.65529 2.02087 5.19062 0.88043 2.65524 5.45552 5.42442 5.15469 5.16815 4.66249 4.12260 1.40813 5.79888 4.77647 195 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 112 2.18892 5.38966 2.64044 1.97751 4.73333 3.65659 3.60437 3.92129 2.10090 3.35469 4.43069 2.33847 4.05005 2.60616 2.77179 2.58383 3.11351 3.51057 5.82316 3.92131 196 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 113 2.81051 5.07767 4.77644 4.29954 2.03535 4.57845 2.23184 3.59557 4.18346 3.18325 4.21755 4.37554 4.93163 4.33627 4.35340 3.88728 3.48134 3.41897 4.49144 0.85916 197 y - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 114 3.22459 2.61128 5.38969 4.79509 3.58979 4.68737 5.03975 1.79213 4.61293 0.89179 2.61919 4.84389 4.96801 4.69100 4.62327 4.02095 3.66625 2.57847 5.40913 4.29402 198 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 115 4.50357 5.94639 4.67261 4.49457 2.97674 4.90740 0.35314 4.75553 4.20979 3.98991 5.25041 4.60971 5.36272 4.62490 4.36557 4.47961 4.76464 4.60938 4.62703 2.51319 199 H - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 116 2.59851 4.33805 2.68311 2.05797 4.71676 3.15802 3.59362 3.65569 2.43439 3.32473 4.42034 2.78736 4.05190 2.70193 2.69422 1.73897 3.11362 3.60918 5.81450 4.40740 200 s - - H
+ 2.68619 4.42226 2.77521 2.73118 3.46355 2.40514 3.72496 3.29355 2.67742 2.69356 4.24691 2.90348 2.73741 3.18131 2.89802 2.37888 2.77521 2.98510 4.58478 3.61505
+ 0.04979 3.09322 5.73865 0.35009 1.21950 0.48576 0.95510
+ 117 2.54785 4.42029 2.89622 2.25922 4.34868 3.66610 3.21799 3.71995 2.27125 3.07920 3.10189 2.25867 4.05899 2.34775 2.56766 2.85682 3.11428 3.36249 5.78309 3.93739 202 n - - T
+ 2.68634 4.42198 2.77524 2.73138 3.46344 2.40486 3.72467 3.29300 2.67713 2.69352 4.24714 2.90371 2.73709 3.18145 2.89825 2.37911 2.77527 2.98532 4.58501 3.61528
+ 0.09842 2.40225 5.73865 1.69597 0.20263 0.48576 0.95510
+ 118 2.53322 5.34393 2.95935 2.59629 3.94657 1.84501 3.63806 4.14023 2.18335 3.64044 4.39013 2.55576 3.77395 2.95784 2.71428 2.21077 3.11477 3.72355 4.68564 4.39095 213 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 119 3.55513 4.24694 5.60079 5.05662 2.60993 4.96071 5.43324 0.97900 4.91818 2.09234 3.80321 5.12225 5.23216 5.06726 4.97588 4.32549 3.79818 1.34455 5.81250 4.64107 214 i - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 120 2.50668 3.55624 4.84676 4.23404 3.24346 4.08398 4.41611 1.66920 4.02684 2.01982 2.79518 4.23489 4.44784 4.16480 3.83668 2.91482 2.83994 1.71230 4.92013 3.32611 215 i - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 121 4.62495 5.94818 4.90176 4.71687 2.80207 5.05504 0.41821 4.71670 4.43975 3.92227 5.21366 4.70109 5.45885 4.74110 4.56151 4.57303 4.86606 4.59605 4.46431 2.05738 216 H - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 122 3.04282 4.16968 3.83274 3.22981 4.12386 3.92565 4.16387 3.45658 2.89535 2.79946 3.52962 3.63885 4.33284 3.40809 0.88367 3.03173 2.91452 3.20781 5.47983 4.24517 217 r - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 123 4.66549 6.56867 0.13049 3.73947 6.20930 4.51726 5.46620 6.15252 4.80154 5.54790 6.65359 4.31602 5.22661 4.77980 5.35908 4.57977 5.04873 5.69924 7.06132 6.05090 218 D - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 124 4.11594 5.30633 6.13178 5.57769 3.73657 5.59693 5.98457 1.50133 5.46568 0.67788 3.07617 5.76705 5.63423 5.36401 5.43088 5.00606 4.33175 2.14525 5.97972 5.01356 219 L - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 125 4.55719 6.24846 4.80697 4.34215 5.94023 4.73956 5.02576 5.52333 0.17090 4.86848 5.87217 4.66859 5.24422 4.23030 3.41495 4.59394 4.77093 5.20290 6.57866 5.65826 220 K - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 126 2.73388 4.87911 3.10327 2.90832 4.07991 3.41413 4.01646 3.20246 2.89177 2.38683 3.78561 3.39051 1.51394 3.22647 3.32105 2.31617 2.81372 3.19214 5.43675 4.15025 221 p - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 127 2.30763 5.39894 2.49711 1.50775 4.74209 3.53358 3.60730 4.22742 2.31483 3.70337 3.89187 2.94609 4.05547 2.65035 3.08133 2.29509 3.12215 3.78862 5.83238 4.42137 222 e - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 128 4.24075 6.04161 4.10323 4.13804 5.66046 4.44992 5.52992 5.77835 4.64675 5.26705 6.30900 0.15130 5.17553 4.91694 4.94682 4.32646 4.70552 5.25421 6.75952 5.61338 223 N - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 129 3.55135 3.88080 5.58388 5.03211 3.05772 4.93598 5.38843 0.81084 4.88763 1.84199 3.74557 5.09695 5.20522 5.02095 4.93631 4.29650 3.79207 1.75582 5.75938 4.60163 224 i - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 130 4.26500 5.46000 6.21355 5.61602 2.31085 5.64571 5.88455 2.68862 5.47780 0.52109 2.36789 5.81754 5.61663 5.25881 5.37169 5.03996 4.45544 2.72136 5.81387 4.88779 225 L - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 131 3.14725 3.80930 5.11896 4.51210 2.75868 4.35237 4.69393 1.48763 4.30885 1.32733 3.15909 4.51494 4.68518 4.42027 4.31553 3.67228 3.37834 1.91515 5.14039 3.60311 226 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 132 2.83132 4.28838 2.02200 2.41335 4.70055 3.12743 3.31546 4.17875 2.06503 3.46693 4.09733 2.49326 4.05387 2.94892 3.07895 2.27711 2.89161 2.90947 5.80603 4.40188 227 d - - E
+ 2.68620 4.42227 2.77521 2.73125 3.46356 2.40515 3.72496 3.29356 2.67743 2.69346 4.24692 2.90348 2.73741 3.18137 2.89794 2.37889 2.77521 2.98513 4.58479 3.61505
+ 0.19179 2.92011 2.11536 0.31959 1.29625 0.48576 0.95510
+ 133 2.77846 5.34345 2.73873 2.12504 4.68884 3.31622 3.10327 4.17503 2.07146 3.64885 4.14408 2.35495 3.55373 2.53396 2.68259 2.30312 2.80970 3.73426 5.77591 4.07717 229 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01122 4.89146 5.61380 0.61958 0.77255 0.46383 0.99121
+ 134 2.76231 5.37627 2.40965 2.30431 4.72103 3.48860 3.46007 4.20680 2.15285 3.68141 4.41704 2.22463 3.54282 2.67483 2.66394 2.48608 2.48229 3.08661 5.80911 4.39830 230 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01030 4.97674 5.69908 0.61958 0.77255 0.42506 1.06054
+ 135 2.88621 4.31580 2.58861 2.52891 4.00821 1.80604 3.64216 3.70404 2.55848 3.01103 3.82083 2.93142 3.28125 2.96153 3.15140 2.63196 2.92652 3.07947 5.65563 3.39061 231 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 136 2.74326 5.32913 2.62872 2.23118 4.20190 3.27586 3.01088 3.39612 2.54602 3.28443 3.99578 2.66732 4.06020 2.45230 2.82728 2.54748 2.65672 2.69485 5.77785 3.49295 232 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 137 2.61635 3.28525 4.16732 3.71739 2.98202 4.03403 4.34546 2.03775 3.50788 1.92540 3.47356 3.38535 3.11745 3.96570 3.52677 3.32696 2.46663 1.86856 4.97202 3.78516 233 v - - E
+ 2.68644 4.42087 2.77438 2.73125 3.46306 2.40580 3.72561 3.29182 2.67742 2.69394 4.24637 2.90298 2.73752 3.18209 2.89809 2.37898 2.77573 2.98487 4.58490 3.61464
+ 0.36530 1.19470 5.73865 2.01193 0.14356 0.48576 0.95510
+ 138 2.92386 3.12674 3.30583 2.50241 4.41812 3.73989 3.57074 3.83865 1.16713 3.42239 3.64701 3.25964 4.12762 3.06518 2.74407 2.94589 3.15200 3.22587 5.64420 3.71460 253 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 139 3.61791 5.07369 5.93139 5.42030 4.01697 5.40165 5.95563 1.06228 5.32659 1.08905 3.76387 5.56598 5.56723 5.42106 5.39317 4.81179 4.11011 1.74432 6.14737 5.05160 254 i - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 140 1.74479 2.79152 4.35686 3.77898 3.55350 2.78668 4.34505 2.08763 3.66685 2.55990 3.56128 3.98833 4.38080 3.89329 3.86150 2.46831 2.34811 2.41028 5.05799 3.86488 255 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 141 4.66549 6.56867 0.13049 3.73947 6.20930 4.51726 5.46620 6.15252 4.80154 5.54790 6.65359 4.31602 5.22661 4.77980 5.35908 4.57977 5.04873 5.69924 7.06132 6.05090 256 D - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 142 4.66482 5.73614 5.86239 5.64956 0.40883 5.43325 4.33355 3.86711 5.42110 2.16428 4.36705 5.11239 5.65371 5.16689 5.27011 4.83252 4.86624 3.98432 3.74189 2.69037 257 F - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 143 3.93699 5.85566 3.02816 3.87037 6.00993 0.21285 5.44927 5.75466 4.70121 5.27717 6.21696 4.31536 4.99427 4.76567 5.12629 4.02226 4.42780 5.10478 6.99282 5.96830 258 G - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 144 2.54355 3.67295 4.73868 4.13265 2.71576 4.06852 3.76754 2.37455 3.94756 1.20416 3.31174 3.74431 4.43365 4.10500 4.00521 2.64259 3.14725 2.29206 4.93223 3.75278 259 l - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03189 5.01631 3.69859 0.61958 0.77255 0.48576 0.95510
+ 145 0.77520 2.86695 4.81978 4.47036 4.95592 3.15951 5.20700 4.36343 4.38394 4.08078 4.90451 4.25075 4.38058 4.58838 4.56864 1.45304 3.34905 3.34992 6.35477 5.22001 260 a - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.07711 4.99453 2.69658 0.61958 0.77255 0.54567 0.86620
+ 146 2.54977 3.79925 3.16699 2.32606 4.48674 3.31547 3.84408 3.47518 1.75582 3.12339 4.25869 2.84258 4.04145 2.96441 2.18943 2.71334 2.91887 2.95414 5.67187 4.30075 261 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.13472 4.92824 2.13029 0.61958 0.77255 0.70219 0.68419
+ 147 2.64685 3.78445 3.06669 2.61534 3.32325 3.67596 3.69246 3.14713 2.01231 2.43193 3.43451 3.16113 4.06301 2.47274 3.08778 2.74475 2.84906 2.65428 5.37440 4.07606 262 k - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.29473 4.80574 1.39802 0.61958 0.77255 0.92027 0.50818
+ 148 2.40579 4.15423 4.25399 3.66267 2.39272 3.57693 3.44550 2.33935 3.03827 1.86796 2.97007 3.83355 4.18573 3.73297 3.67827 3.10851 2.93289 2.21754 4.76738 2.96352 263 l - - .
+ 2.68635 4.42219 2.77489 2.73146 3.46367 2.40530 3.72500 3.29419 2.67720 2.69370 4.24630 2.90362 2.73727 3.18122 2.89818 2.37860 2.77478 2.98583 4.58472 3.61420
+ 0.77167 0.63015 5.24955 1.50734 0.25038 0.20147 1.70117
+ 149 2.68930 5.13793 2.99383 2.28756 4.12167 3.02811 3.40047 2.83046 2.53990 2.67433 3.91490 2.66806 3.85841 2.95123 3.08518 2.54554 2.43488 3.14237 4.83794 3.11842 281 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 150 2.67960 3.59834 3.08049 2.32634 4.00400 2.85568 3.65072 3.26198 2.22635 2.80014 3.89773 3.03566 3.90780 2.84131 2.77630 2.59674 2.54121 2.94346 4.66327 3.60288 282 k - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 151 2.78407 5.36932 2.80723 2.38070 3.95652 3.28210 3.31902 3.80407 2.38757 3.23090 4.41260 2.26860 2.87333 2.94776 2.55475 2.11230 2.82314 3.31603 5.80800 4.40313 283 s - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 152 2.55066 5.37311 2.42428 2.58328 4.70981 2.65546 3.66067 3.46611 2.34139 3.39818 4.41598 2.44705 3.58966 2.48003 2.87086 2.30355 2.92043 3.58081 5.81084 3.32103 284 s - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 153 2.61131 5.36709 3.05324 2.00706 4.70125 2.53001 3.45141 4.17959 2.46541 3.54879 4.41063 3.13225 3.27183 2.67970 2.77280 2.14590 2.62504 2.97295 5.80635 3.79465 285 e - - S
+ 2.68619 4.42226 2.77520 2.73124 3.46320 2.40514 3.72495 3.29355 2.67742 2.69356 4.24691 2.90348 2.73740 3.18147 2.89802 2.37888 2.77520 2.98519 4.58478 3.61504
+ 0.03620 3.43177 5.73865 0.40966 1.09027 0.48576 0.95510
+ 154 2.80870 4.76397 2.82688 2.35901 3.53520 3.31737 3.24083 3.53679 2.31494 2.98485 3.52265 2.69923 3.15465 2.90046 2.56489 2.40361 2.83318 3.04461 5.74293 3.76697 287 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 155 2.38638 3.55872 3.84850 3.27925 3.07902 3.89951 3.49984 3.07191 2.87600 2.13071 2.79826 2.94436 3.28103 3.24012 3.30127 2.77627 2.52689 2.66914 5.17020 2.84075 288 l - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 156 2.88266 4.79637 2.63708 2.49106 4.69372 3.27452 3.02757 4.17056 2.31920 3.54781 3.84892 2.54158 3.83133 2.71114 2.83815 2.34796 2.07167 3.53868 4.84477 3.26548 289 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 157 2.55115 5.22307 2.81541 2.42597 3.84088 2.72211 3.45978 3.70939 2.65113 3.50012 4.03956 3.00145 3.26637 2.92366 3.12986 2.10982 2.09681 2.95270 4.42058 4.32902 290 t - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 158 2.79383 4.53543 3.94528 3.00256 2.28876 3.25886 4.19260 2.53698 3.31063 2.13485 3.51266 3.25465 3.61933 3.02975 2.60672 3.04108 3.13630 2.22820 5.12884 3.03437 291 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 159 2.54133 2.27249 3.62507 3.14565 3.48798 3.47382 4.20805 2.87324 3.24770 2.61629 3.62417 3.76153 4.31084 3.45605 3.15192 3.19594 2.77273 1.44309 5.11140 3.89714 292 v - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 160 2.50560 4.02210 4.21483 3.69251 4.03927 0.87585 4.50859 3.18042 3.62456 3.12203 4.01557 3.91946 4.34666 3.89680 3.91281 2.66630 3.23503 2.52015 5.49804 3.97346 293 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 161 2.98792 5.00679 3.18026 3.47531 5.09253 3.65988 4.75357 4.53531 3.72802 4.18133 4.99276 3.79669 4.37930 3.97717 4.12874 1.60941 0.74054 3.97784 6.39182 5.11951 294 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 162 2.69840 5.26022 3.00961 2.31122 4.20998 3.68086 3.63617 3.20701 2.41779 2.58849 4.31499 2.98486 2.62271 2.99075 2.13729 2.36313 3.11573 3.42385 5.72545 3.54571 295 r - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 163 2.71301 5.29924 2.59488 2.14743 3.52695 3.04037 3.28275 4.06670 2.61594 3.34508 4.35002 2.84026 3.31113 2.97459 2.36266 2.86533 2.70674 3.41928 3.03699 3.23042 296 e - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 164 4.65993 5.73598 5.69662 5.49898 1.97465 5.32012 3.31709 4.36240 5.29326 3.66395 4.92323 4.93743 5.59573 5.06816 5.17473 4.69695 3.41633 4.25844 2.61302 0.51590 297 Y - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 165 2.46851 3.63596 4.34730 3.76113 3.49978 4.00900 4.30977 2.55613 3.41377 2.11254 1.89168 3.40620 4.37893 3.86942 2.23584 3.08926 3.14320 2.13937 5.00600 3.81292 298 m - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 166 0.54633 4.79516 4.59072 4.34047 5.33605 3.22550 5.27451 4.80651 4.37656 4.47607 5.24769 4.21379 3.02084 4.58677 4.60871 1.81435 3.40538 4.05386 6.66459 5.53199 299 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 167 3.08666 5.02380 4.02349 3.92167 5.10908 3.73669 5.07487 4.62556 4.04836 4.33998 5.22795 3.34786 0.41351 4.38870 4.30726 3.26072 3.60085 3.40472 6.47905 5.20179 300 P - - H
+ 2.68622 4.42144 2.77523 2.73111 3.46358 2.40517 3.72498 3.29358 2.67745 2.69359 4.24694 2.90351 2.73743 3.18126 2.89786 2.37891 2.77523 2.98522 4.58481 3.61507
+ 0.03484 3.47295 5.73865 0.99675 0.46057 0.48576 0.95510
+ 168 3.66837 6.19086 2.84947 0.45189 5.55161 3.90523 4.43200 5.09782 3.30487 4.55035 5.42336 3.03786 4.53514 3.60153 3.37398 3.54999 3.95969 4.65772 6.64024 5.17650 305 E - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 169 2.79774 4.32598 4.68241 3.67608 3.42171 4.06471 4.38713 2.01470 3.90321 1.87174 3.44282 4.15860 4.43014 3.77035 3.25202 3.36713 2.95239 1.31877 3.77234 3.76466 306 v - - H
+ 2.68603 4.42242 2.77519 2.73104 3.46342 2.40506 3.72511 3.29371 2.67728 2.69322 4.24707 2.90364 2.73756 3.18163 2.89801 2.37893 2.77519 2.98535 4.58494 3.61520
+ 0.12919 2.22240 4.35495 1.23224 0.34480 0.48576 0.95510
+ 170 2.91184 3.76308 4.76588 4.15799 3.39752 4.06920 3.82796 1.60071 3.96642 1.39613 3.17824 3.65225 4.43387 4.11848 4.01348 2.94594 3.14403 2.21737 4.92444 3.43929 311 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00999 5.00664 5.72898 0.61958 0.77255 0.51297 0.91308
+ 171 2.62785 5.06480 3.29796 2.67561 3.73804 3.41086 3.92577 3.21358 2.32640 2.15096 3.31180 2.55443 4.11004 2.47045 2.33927 2.70318 3.11578 3.12852 5.57146 4.24107 312 l - - C
+ 2.68631 4.42245 2.77511 2.73076 3.46350 2.40522 3.72547 3.29356 2.67765 2.69366 4.24573 2.90389 2.73738 3.18142 2.89826 2.37846 2.77520 2.98520 4.58530 3.61473
+ 0.62427 1.87899 1.16602 1.98855 0.14722 0.46912 0.98231
+ 172 2.60166 5.18307 2.62016 2.19793 3.35206 2.39740 3.57105 3.96340 2.18128 3.47543 4.23188 3.01161 3.92489 2.82990 2.86326 2.33987 2.67701 3.55746 5.63416 3.78538 327 k - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01428 4.65191 5.37425 0.61958 0.77255 0.24611 1.52250
+ 173 2.37600 3.94341 2.81761 2.45806 4.08381 2.38833 3.32666 4.15213 2.47322 3.64753 4.39446 2.71786 3.74359 2.39493 2.76163 2.38666 3.00597 3.01776 5.79219 3.82026 328 a - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00998 5.00778 5.73012 0.61958 0.77255 0.47101 0.97916
+ 174 2.81816 4.87774 2.88922 2.34131 3.91699 3.47934 3.84840 3.76601 2.22767 3.10881 4.41163 2.46519 2.75598 2.51039 2.43545 2.43680 2.76354 3.54179 5.80719 3.84984 329 k - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 175 2.74169 5.33416 2.58184 2.32653 3.61666 2.33545 3.50275 4.12419 2.36762 3.50261 3.56274 2.91332 3.07814 2.74477 2.96926 2.79421 2.92848 3.32496 5.78164 2.72284 330 e - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 176 2.48397 4.72191 2.72922 2.94719 3.45604 3.83733 2.73484 2.72590 3.03376 2.94128 3.81928 3.51045 4.21965 3.13222 3.31573 2.84267 3.12967 2.71705 3.94971 1.76193 331 y - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 177 2.88858 5.15756 2.48812 2.69267 3.68939 2.20273 3.90720 3.84889 2.69072 3.17648 4.22648 3.21985 3.19313 3.04303 3.16266 2.07644 2.02474 3.50391 5.64990 3.69862 332 t - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 178 2.44412 5.27089 3.18567 2.52594 4.01181 3.49400 3.20300 3.68711 2.26882 2.99802 4.32458 3.16791 2.73532 2.67304 2.47574 2.35896 2.41445 3.31659 5.73361 3.79657 333 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 179 2.27957 5.36842 3.14470 2.24142 4.70283 3.35867 3.70433 4.18054 1.84880 3.00297 4.41216 3.13478 2.50109 2.87247 2.49374 2.50485 2.88881 3.75338 5.80713 4.40386 334 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 180 2.25487 3.19836 3.67383 3.53894 3.58335 3.60706 4.24810 2.30247 3.45618 2.57768 3.58074 3.40343 4.33674 3.48890 3.71724 2.25302 2.94661 1.56396 5.07167 3.86608 335 v - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 181 3.32488 6.23611 0.30142 2.99559 5.85936 3.97225 4.81661 5.46625 4.07634 5.00781 5.98660 3.57219 4.70996 4.04099 4.76451 3.76774 4.26196 4.95940 7.04785 5.56474 336 D - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 182 2.97530 4.34655 4.92112 4.31006 3.42469 4.15298 4.48903 1.67409 4.10270 2.14170 2.44181 4.30839 4.51041 4.23558 4.11915 3.46567 2.80277 1.45020 3.28394 3.56694 337 v - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 183 4.60767 5.71652 5.61554 3.89031 2.18526 5.28181 4.15190 4.32304 5.18037 3.62888 4.88484 4.90634 5.56392 5.01906 5.10312 4.65700 4.81381 4.22147 0.60655 1.74323 338 W - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 184 1.30551 4.78823 4.65738 4.37945 5.36630 2.58206 5.28849 4.84019 4.38318 4.50739 5.27020 4.22569 4.39579 4.59600 4.61395 0.79404 2.89139 4.06528 6.68751 5.56026 339 s - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 185 2.44153 3.17932 4.87400 4.25972 2.53121 4.09082 4.42403 2.33144 4.04748 1.34403 2.92510 4.24940 4.45392 4.18053 4.05982 3.14600 3.15398 2.13810 4.92017 3.14864 340 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 186 2.22507 4.96728 4.63623 4.63233 5.66307 0.33314 5.62287 5.16416 4.86793 4.86816 5.66661 4.43512 4.57282 5.01497 4.99264 3.26151 3.63533 4.32703 6.92990 5.89905 341 G - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 187 2.93009 2.13614 4.95885 4.35253 3.48038 4.19799 4.54424 1.68794 4.14925 1.93394 3.18432 4.35359 4.55452 4.28834 4.17024 3.34008 3.23972 1.60527 5.03746 3.47367 342 v - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 188 3.21831 4.55127 5.17022 4.58630 3.70338 4.47717 4.86313 1.30610 4.40976 1.92114 2.79907 4.62299 4.81179 4.56490 4.45688 3.52794 2.67243 1.42404 5.34369 4.16408 343 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 189 2.77853 3.56970 4.91220 4.29933 2.66878 4.13468 4.46922 2.12981 4.08926 1.13811 3.14072 4.29275 4.49323 4.21981 4.10205 3.44689 2.88537 2.20246 4.95897 3.46211 344 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 190 2.08301 4.31008 4.80905 4.20025 2.66597 4.08391 3.54227 2.07553 4.00182 2.35024 3.19529 4.21899 4.44796 4.14611 4.03654 3.39206 3.15615 2.32332 2.91148 1.86433 345 y - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 191 2.65126 3.79080 3.03118 1.37895 4.54227 3.68257 3.87660 3.27048 2.56225 3.53374 4.30787 2.88399 4.07460 2.72714 3.11894 2.49943 2.86114 3.20681 5.71940 3.61825 346 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 192 2.75949 4.33120 4.86063 4.24972 2.93412 4.11800 4.44873 2.58063 4.04775 1.34098 1.86205 4.26240 4.47769 4.18564 4.07448 3.30982 2.87183 2.17494 4.95131 3.25026 347 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 193 2.13730 3.34433 4.84746 4.23449 2.67079 4.08305 4.41495 2.45417 4.02682 1.45586 2.95446 4.23448 4.44687 4.16424 3.65241 3.39295 2.78239 2.10310 4.91833 3.10946 348 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 194 2.61714 3.04119 3.51958 2.50105 3.16562 3.44068 4.02999 3.26384 2.78703 2.46125 3.90521 2.94061 4.18669 3.26384 2.94427 2.45451 1.92365 2.96026 5.36672 3.77569 349 t - - H
+ 2.68592 4.42131 2.77530 2.73134 3.46364 2.40523 3.72505 3.29364 2.67751 2.69365 4.24624 2.90357 2.73750 3.18157 2.89769 2.37886 2.77510 2.98507 4.58487 3.61513
+ 0.08274 2.77459 4.07273 1.24373 0.34011 0.48576 0.95510
+ 195 2.74009 5.38236 2.60734 2.58658 4.30151 1.49346 3.57775 4.19577 2.06867 3.68256 4.42710 2.84258 4.06100 2.86136 2.79826 2.78642 3.12785 3.76776 5.82019 4.41533 355 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02515 5.00240 4.01100 0.61958 0.77255 0.52459 0.89600
+ 196 2.87057 4.15783 2.81932 2.15097 3.67482 3.00161 3.44561 3.53712 2.01194 3.52030 4.39830 2.84675 4.04172 2.62971 2.18111 2.65254 2.90372 3.46034 5.79407 3.92999 356 k - - S
+ 2.68632 4.42239 2.77496 2.73101 3.46368 2.40527 3.72508 3.29339 2.67739 2.69369 4.24616 2.90361 2.73734 3.18160 2.89815 2.37901 2.77533 2.98486 4.58491 3.61430
+ 0.06990 2.74572 5.70978 1.46974 0.26135 0.43968 1.03351
+ 197 2.53761 4.57755 3.85895 3.05555 3.06219 3.90225 3.89097 2.90555 3.23603 1.98376 3.43681 3.14844 2.18635 3.28921 3.56902 2.76101 2.38583 2.48063 5.16546 3.65117 363 l - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 198 2.94035 4.49377 4.16973 3.59341 3.59928 3.99457 4.28692 2.57573 3.48228 2.11382 3.59630 3.88641 1.19333 3.75706 3.46613 3.08341 3.17527 2.51467 5.10025 3.66586 364 p - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 199 2.95410 3.97958 4.76382 4.16399 1.23466 4.10162 4.38107 2.78567 3.65586 2.19089 3.46719 4.20671 3.78920 4.13156 4.03525 3.25126 3.18603 2.50296 2.73984 2.86766 365 f - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 200 2.72297 4.82530 2.62940 2.35446 3.83755 3.31971 3.71413 4.17131 2.26174 3.54363 4.14174 3.02369 2.60946 2.49179 2.66057 2.21727 2.99115 3.74587 4.55596 3.10965 366 s - - S
+ 2.68620 4.42227 2.77522 2.73112 3.46340 2.40515 3.72496 3.29334 2.67743 2.69357 4.24692 2.90349 2.73742 3.18148 2.89803 2.37889 2.77522 2.98520 4.58479 3.61505
+ 0.07731 2.84051 4.13492 0.30572 1.33404 0.48576 0.95510
+ 201 2.63880 5.38435 2.63657 2.22720 4.72697 1.94780 3.15235 3.87964 2.57669 3.68860 4.42577 2.57921 3.16991 2.74291 2.86900 2.50219 2.85278 3.77370 5.81843 4.40865 368 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.52175 0.90012
+ 202 2.40102 4.71375 2.46996 2.13243 4.71840 3.11745 3.05416 3.48265 2.25142 3.16134 4.41932 2.93828 3.25177 2.60824 2.79040 2.58260 2.90071 3.38079 5.81277 4.40438 369 e - - S
+ 2.68658 4.42180 2.77453 2.73123 3.46394 2.40505 3.72421 3.29333 2.67765 2.69382 4.24730 2.90354 2.73686 3.18110 2.89829 2.37906 2.77522 2.98525 4.58428 3.61543
+ 0.55463 1.48984 1.60791 1.39890 0.28351 0.52175 0.90012
+ 203 2.69338 5.29005 2.51143 2.25105 4.62988 2.84270 3.49832 3.48405 2.27737 3.31427 4.33211 2.56706 3.20350 2.85310 2.67590 2.21378 2.73620 3.67787 5.72586 4.31806 375 s - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01250 4.78398 5.50633 0.61958 0.77255 0.95212 0.48763
+ 204 2.65942 5.19894 2.69156 2.28179 3.77027 3.19251 3.77484 3.06173 2.43464 2.99400 3.94013 2.58274 3.44930 2.63512 2.62020 2.46578 2.71730 3.35179 5.65696 3.80565 376 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01250 4.78398 5.50633 0.61958 0.77255 0.77169 0.62033
+ 205 2.38920 5.21254 2.73488 2.26876 4.51445 3.29559 3.03245 3.05648 2.42252 2.83088 3.97624 2.72691 3.66747 2.74292 2.65924 2.79642 2.87825 3.04317 5.67196 3.47007 377 e - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01186 4.83615 5.55849 0.61958 0.77255 0.33713 1.25111
+ 206 2.65422 4.48489 1.88534 2.29942 4.71042 3.12833 3.84224 3.67843 2.58000 3.67468 4.41498 2.22848 4.04754 2.86157 2.64414 2.33478 2.73698 3.75923 5.80928 4.40246 378 d - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.52175 0.90012
+ 207 2.52228 5.35256 2.79874 2.27245 4.68298 3.15080 3.25420 3.81263 2.42135 3.03021 2.98061 3.02733 3.41549 2.09266 2.89624 2.43800 3.03420 3.22791 5.79412 4.39217 379 q - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.52175 0.90012
+ 208 2.88352 5.03264 3.01718 2.64158 3.36791 3.41419 3.67586 2.82361 2.46533 2.06980 3.25199 2.87105 3.91016 2.67457 2.54739 2.67076 3.11488 3.35644 5.54543 3.24074 380 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.52175 0.90012
+ 209 2.31106 5.21929 3.20358 2.11286 3.58411 3.54755 3.12693 3.74178 2.35878 3.37262 4.27754 3.18132 3.64073 2.21825 2.83044 2.63943 3.03559 2.71879 4.50670 3.34948 381 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01003 5.00344 5.72579 0.61958 0.77255 0.46390 0.99109
+ 210 2.74907 4.02445 4.23598 3.43708 3.16042 3.98772 3.66116 2.29352 2.78065 1.91975 2.65717 3.64306 4.00461 3.79624 2.62994 3.12682 2.72367 2.05105 5.03295 3.83444 382 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 211 2.79706 4.32223 4.14412 4.07508 2.44930 4.05985 3.54709 1.67401 3.90204 2.17979 2.94629 3.31750 4.42562 4.07034 3.98057 2.91878 2.88141 2.01026 4.94063 2.95520 383 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 212 2.43063 3.51667 2.84063 2.33381 3.23751 3.53757 3.64461 3.61354 2.52297 3.04234 3.80037 3.02528 3.31294 2.77439 2.36706 2.71893 3.04140 2.71650 5.64517 3.47973 384 e - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 213 2.54995 5.35768 3.14585 2.23433 4.68798 3.33616 3.38625 3.80986 2.09254 2.85705 3.68757 2.56176 4.05535 2.40160 2.38927 2.57618 3.04385 3.36418 5.79929 3.79887 385 k - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 214 2.66499 5.02053 2.80345 2.59207 4.23983 3.19081 3.94632 1.95336 2.43621 2.96229 3.77095 2.92719 4.12615 3.11304 2.86357 2.94448 2.42822 2.54184 5.53679 4.21766 386 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 215 2.79062 4.84420 3.48859 2.83007 4.02200 3.06268 4.01637 2.98055 2.36084 1.68419 3.06982 3.40535 3.56488 2.89781 2.78978 2.64270 2.97298 2.81255 5.39215 4.11258 387 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 216 2.78422 4.40067 2.87114 2.38957 4.66317 2.42774 3.11725 3.68493 2.29738 3.11118 3.80555 3.07548 3.38861 2.66839 2.52841 2.36297 2.74889 3.71883 4.85618 3.72852 388 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04975 5.01631 3.17248 0.61958 0.77255 0.48576 0.95510
+ 217 2.55009 3.88585 3.08502 2.47179 4.52328 2.60499 3.86026 3.74333 2.31088 3.21633 3.94275 3.03087 2.50945 2.97834 2.41589 2.69163 2.38722 3.38360 5.70135 4.11095 389 k - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01030 4.97686 5.69921 0.61958 0.77255 0.59090 0.80705
+ 218 2.71816 5.35510 2.47492 2.28903 4.69101 3.44039 3.67059 2.92462 2.15295 3.03900 4.39818 2.98975 2.40750 2.74839 2.76016 2.49540 2.85213 3.74081 5.79327 4.38792 390 k - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02103 4.97686 4.27462 0.61958 0.77255 0.59090 0.80705
+ 219 2.59242 4.56547 3.37418 3.24570 3.28039 3.87349 3.78552 2.80260 2.91515 1.85640 3.67045 2.94464 3.03710 3.48913 3.31352 2.93163 2.57101 2.12270 4.60315 3.29903 391 l - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01041 4.96623 5.68858 0.61958 0.77255 0.61678 0.77584
+ 220 2.76552 5.35116 2.75065 2.09233 4.26840 3.39661 3.23930 3.45666 2.13782 2.93921 3.69074 2.78256 2.85112 2.85423 2.61182 2.41762 3.01864 3.73701 5.78920 4.16743 392 e - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01041 4.96623 5.68858 0.61958 0.77255 0.61678 0.77584
+ 221 2.56616 4.88573 3.26662 2.33696 2.41520 3.27403 3.41068 2.92250 2.70761 2.68623 3.97070 3.19787 3.38122 3.16656 2.79903 2.47364 2.99470 2.86843 4.82552 3.32054 393 e - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01041 4.96623 5.68858 0.61958 0.77255 0.61678 0.77584
+ 222 2.62567 5.35084 2.04845 2.35215 4.39252 3.47212 3.16243 3.98892 2.45186 3.65226 3.66396 2.66846 2.63580 2.82810 3.05661 2.22708 2.99549 3.54011 5.78899 3.92777 394 d - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03667 4.96623 3.53930 0.61958 0.77255 0.61678 0.77584
+ 223 2.86103 4.03193 3.18635 2.38909 3.31435 3.61153 3.49109 2.70908 2.69769 2.69388 3.88535 3.22191 3.67076 3.11276 2.73635 2.49324 3.00545 2.72730 2.94731 2.96802 395 e - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01875 4.94025 4.47244 0.61958 0.77255 0.67631 0.71028
+ 224 2.62521 5.12447 2.77972 2.44738 3.31605 3.53418 3.86652 3.33309 2.47319 3.03557 4.18886 3.10134 2.42408 2.60018 2.70100 2.64509 2.92363 3.22521 3.41935 3.46519 396 p - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.05901 4.93227 2.99396 0.61958 0.77255 0.69360 0.69269
+ 225 2.68343 5.20702 2.88582 2.22963 3.55567 3.45903 3.65367 3.49248 2.11994 2.97314 4.26172 2.80968 3.57686 2.44336 3.06162 2.53581 2.67303 3.18308 3.73101 3.66292 397 k - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01130 4.88456 5.60691 0.61958 0.77255 0.78866 0.60597
+ 226 2.68707 4.98468 2.82158 2.38405 3.75917 3.36024 3.65392 3.18317 2.38508 2.73942 3.76303 3.22111 3.36652 3.04584 2.96704 2.31757 2.64759 2.95752 3.21600 3.40268 398 s - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.11345 4.88456 2.30573 0.61958 0.77255 0.78866 0.60597
+ 227 2.79298 3.84213 2.48108 2.52210 3.99851 3.60747 3.12972 3.13545 2.48018 3.05991 4.13768 2.83211 3.54520 2.93964 2.41588 2.35619 2.76810 2.97839 5.56015 3.44494 399 s - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02807 4.78362 3.94704 0.61958 0.77255 0.95264 0.48731
+ 228 2.58191 4.56682 2.77742 2.37170 4.46635 3.58143 3.77449 3.50815 2.36445 2.67587 4.22448 2.86502 2.73607 2.80387 2.79297 2.07848 2.75446 3.53442 5.63386 3.74575 400 s - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.14447 4.76826 2.07130 0.61958 0.77255 0.97412 0.47405
+ 229 2.74120 5.02625 2.90214 2.38037 3.96892 2.81361 3.75340 3.09744 2.29181 2.85276 3.79351 2.85134 3.31773 2.88600 2.57247 2.48932 2.74923 2.81409 5.51153 4.15648 401 k - - .
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02950 4.63827 3.94280 0.61958 0.77255 1.12880 0.39071
+ 230 2.65814 5.03703 2.72915 2.44094 4.30481 3.19996 3.74471 3.73960 2.51991 2.72378 3.12113 3.05398 2.98987 2.79382 2.49179 2.12708 2.96796 3.38544 5.51898 3.52938 402 s - - .
+ 2.68724 4.42293 2.77612 2.73159 3.46162 2.40699 3.72369 3.29398 2.67731 2.69321 4.24701 2.90285 2.73662 3.18257 2.89624 2.37860 2.77511 2.98573 4.58252 3.61251
+ 0.60323 0.80254 5.34581 2.99471 0.05135 0.22221 1.61320
+ 231 2.51767 5.38833 2.69504 1.91983 4.73145 3.65677 3.84405 3.51135 2.26714 3.33248 4.42951 2.74739 2.83044 2.63263 2.69535 2.26534 2.89575 3.77792 5.82218 4.12814 442 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 232 2.61324 5.33087 2.55247 1.71577 3.78905 3.51981 3.85697 4.11872 2.53837 3.37618 3.68276 2.71899 3.50504 2.96215 2.76975 2.43182 2.62759 3.19721 4.83386 4.08215 443 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 233 1.85315 2.66076 4.74963 4.14369 2.72361 2.76389 4.40211 2.66580 3.95769 1.60680 3.08425 4.19191 4.43908 4.11400 4.01342 3.37949 2.94810 2.35782 4.93743 3.75833 444 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 234 2.54113 3.93957 3.31567 2.58263 3.59686 3.36801 3.93655 2.84244 1.77469 2.55244 4.12290 3.02474 4.11900 2.54032 2.70090 2.93506 2.79964 3.23719 5.55956 3.97978 445 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 235 2.66035 5.38903 1.80529 2.16718 4.22724 3.25823 3.17680 4.00903 2.28647 3.50730 4.43018 2.97613 4.05032 2.48614 2.98498 2.31241 3.11375 3.77870 5.82277 3.97909 446 d - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 236 3.21254 4.56529 5.14365 4.53738 1.97526 4.40976 4.73239 2.19759 4.34073 1.04052 3.41232 4.55986 4.72994 4.44093 4.35221 3.72900 3.00622 2.20314 5.16040 3.53582 447 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 237 2.97518 4.05135 5.35921 4.78478 3.77817 4.66169 5.06989 1.35059 4.61468 1.50253 2.60400 4.82061 4.97178 4.75525 4.65269 4.00168 3.59517 1.52175 5.50364 4.33590 448 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 238 2.63113 4.16111 2.70523 2.01221 4.32546 2.89528 3.69801 3.91463 1.97992 3.37990 4.41866 2.72468 4.05215 2.88390 2.65380 2.44936 2.78930 3.52828 5.81309 3.68713 449 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 239 2.79532 4.56741 2.59886 2.26653 4.72524 2.97326 3.84498 4.20852 1.87988 3.68761 4.42563 2.67816 4.05093 2.72680 2.26697 2.39445 3.11354 3.44147 4.06926 3.70096 450 k - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 240 2.76031 1.91137 4.93344 4.32897 3.47342 4.21043 4.55379 2.12811 4.13437 1.60981 2.11111 4.35327 4.56463 4.27495 4.16872 3.52442 2.73881 2.49904 5.05160 3.88034 451 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 241 3.00579 3.43594 4.91160 4.30236 2.88535 4.17356 4.48924 2.41412 3.62991 0.97514 3.41700 4.31537 4.52645 4.23058 4.12367 3.48482 3.23680 2.59853 2.70167 3.78558 452 l - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 242 2.51291 3.86266 2.42773 2.26878 4.71076 3.65927 3.14908 3.51790 2.32370 3.67561 4.41657 2.44903 4.05255 2.58104 2.64695 2.72413 2.48024 3.27065 5.81133 3.77060 453 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 243 2.89024 4.99098 3.22187 2.69841 3.16242 3.74556 3.43367 3.45008 2.12873 2.47972 3.65551 3.30484 3.00902 2.69329 2.47140 2.87653 2.77051 2.80352 4.74384 3.09104 454 k - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 244 2.75442 4.59220 1.48443 2.55169 4.69407 3.66624 3.85987 4.16899 2.26580 3.66358 4.41104 2.16093 4.06270 2.96232 2.94350 2.69711 3.00639 3.21953 5.80766 4.40610 455 d - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 245 2.53666 4.51809 3.31495 2.50094 3.81458 3.47863 3.66745 3.68842 2.74796 3.30408 3.76297 2.90283 1.45947 2.98944 2.97069 2.84711 3.12065 2.90248 5.56105 4.23506 456 p - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 246 2.18867 5.36299 2.90524 2.21328 4.32931 3.53924 3.49382 3.97251 2.24621 3.14962 3.99253 2.78034 3.78478 2.54072 2.85251 2.30318 2.70173 3.25844 5.80328 3.47734 457 a - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 247 2.48590 4.36945 2.67418 2.22639 4.72760 3.65776 3.84501 4.21118 1.68322 3.11616 4.42723 3.02530 4.05117 2.52411 2.40832 2.54354 2.78662 3.77464 5.82017 4.41136 458 k - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 248 3.97870 5.88109 4.77637 3.79584 5.10245 4.51923 4.26030 4.68907 2.25479 4.07008 4.99673 4.06985 4.83329 3.42182 0.45649 3.98836 4.07883 4.42272 3.45519 4.78623 459 R - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 249 2.59820 4.04607 4.60274 4.00452 3.26886 3.61184 4.36773 2.06089 3.84570 1.56372 3.45362 4.11687 2.06890 4.02734 3.95003 2.68390 3.14561 2.58630 4.40258 3.38622 460 l - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04987 5.01631 3.16967 0.61958 0.77255 0.48576 0.95510
+ 250 2.79362 5.19179 3.01710 2.75300 4.64905 2.77281 4.01085 4.10036 2.79939 3.46822 4.43166 2.61914 4.12461 3.14023 3.27668 1.68833 1.53351 3.69065 5.84113 4.47617 461 t - - T
+ 2.68631 4.42192 2.77519 2.73130 3.46353 2.40482 3.72508 3.29367 2.67738 2.69360 4.24703 2.90360 2.73753 3.18148 2.89804 2.37867 2.77518 2.98532 4.58490 3.61498
+ 0.12278 2.37863 3.77824 1.17468 0.36950 0.42506 1.06054
+ 251 1.47902 3.78300 4.72209 4.11644 2.74562 3.65840 4.38345 2.02614 3.93274 2.07959 3.21794 4.17061 3.49702 4.09137 3.99270 2.98272 3.05871 2.38788 4.48487 3.74373 467 a - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01009 4.99737 5.71972 0.61958 0.77255 0.53813 0.87669
+ 252 2.38222 4.71734 2.84513 2.05232 4.42547 3.25385 3.43556 4.19285 2.14440 3.09056 3.51596 2.80436 3.18490 2.67888 2.63294 2.69832 2.67125 3.58577 5.80764 4.40015 468 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01009 4.99737 5.71972 0.61958 0.77255 0.45436 1.00747
+ 253 2.65797 4.06542 2.63237 1.57032 4.71890 3.65831 3.45654 4.20087 2.52289 3.68238 4.00276 3.00654 3.59507 2.12286 2.86428 2.58695 3.11362 3.45316 5.81563 3.91003 469 e - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 254 1.93383 3.77543 4.87213 4.26567 3.27005 3.35948 4.48352 1.60295 4.06924 1.71770 3.29328 4.28554 4.50523 4.21524 4.10410 3.45599 3.20183 2.00553 4.99383 3.81574 470 i - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 255 2.91099 3.35807 4.39311 3.80506 3.12662 3.41984 4.32058 2.74098 2.62412 1.35983 2.89439 3.70896 4.38574 3.55146 3.43970 3.02120 3.14303 2.30767 4.99433 3.18557 471 l - - H
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 256 2.62697 4.23577 2.94369 2.01671 4.73311 3.52212 3.12192 4.21804 1.98366 3.41966 4.43054 2.33684 4.05005 2.29561 2.80226 2.65814 2.90658 3.41449 5.82302 4.41298 472 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.48576 0.95510
+ 257 2.67425 5.24257 2.69003 2.64384 4.09422 3.68496 1.59772 3.97575 2.52719 3.06621 3.97630 3.17995 4.07682 2.88982 2.86815 2.31165 2.78826 3.60139 5.71188 4.10399 473 h - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.18941 5.01631 1.79622 0.61958 0.77255 0.48576 0.95510
+ 258 2.81850 5.23743 2.76502 2.35780 4.54654 3.39495 3.79640 3.57339 2.36240 3.35446 4.28834 3.08690 1.61434 2.83455 2.79066 2.56844 3.04975 3.37601 5.69198 4.30446 474 p - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01183 4.83873 5.56107 0.61958 0.77255 0.86853 0.54398
+ 259 3.22678 4.58175 4.94227 4.40609 1.73776 4.31983 4.20406 3.01156 4.21650 2.23279 3.33965 4.33985 4.66520 3.80636 4.24184 3.63704 3.45535 2.61441 1.69956 1.91736 475 w - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01183 4.83873 5.56107 0.61958 0.77255 0.30436 1.33787
+ 260 2.99670 4.36610 4.95290 4.33956 1.72799 3.71830 4.50360 1.92619 4.12878 1.69258 2.79907 4.33234 4.52551 4.25179 4.13733 3.48573 3.22794 1.98896 4.25850 3.81122 476 l - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00667 5.01308 * 0.61958 0.77255 0.00000 *
+//
--- /dev/null
+HMMER3/f [3.1b1 | May 2013]
+NAME fn3
+ACC PF00041.13
+DESC Fibronectin type III domain
+LENG 86
+ALPH amino
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Fri Jun 20 08:22:31 2014
+NSEQ 106
+EFFN 11.415833
+CKSUM 3564431818
+GA 8.00 7.20
+TC 8.00 7.20
+NC 7.90 7.90
+STATS LOCAL MSV -9.4043 0.71847
+STATS LOCAL VITERBI -9.7737 0.71847
+STATS LOCAL FORWARD -3.8341 0.71847
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.70330 4.91262 3.03272 2.64079 3.60307 2.84344 3.74204 3.07942 2.79841 2.65364 4.14864 2.95826 2.87120 3.02176 2.96125 2.44783 2.59757 2.57680 4.02726 3.21526
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.00000 *
+ 1 3.16986 5.21447 4.52134 3.29953 4.34285 4.18764 4.30886 3.35801 3.70246 2.11675 4.32057 4.32984 0.76706 3.91880 4.22437 3.23552 3.21670 2.88223 5.80355 3.93889 1 p - - -
+ 2.68629 4.42236 2.77530 2.73088 3.46365 2.40512 3.72505 3.29365 2.67737 2.69316 4.24701 2.90358 2.73734 3.18157 2.89812 2.37898 2.77517 2.98515 4.58488 3.61514
+ 0.09796 2.38361 6.81068 0.10064 2.34607 0.48576 0.95510
+ 2 2.70230 5.97353 2.24744 2.62947 5.31433 2.60356 4.43584 4.79731 3.17221 2.95090 5.01531 3.26630 2.09873 3.30219 3.34190 1.45782 3.14099 3.57507 6.40877 4.25623 3 s - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 3 1.38116 5.98285 3.50784 2.54546 5.32790 3.48945 4.43311 4.81385 2.38773 3.98773 5.02352 3.27895 1.92260 2.69012 2.96119 2.64228 3.29228 3.29618 6.41555 4.20553 4 a - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 4 3.32856 5.10403 4.47046 4.60386 4.23079 4.75438 5.09647 2.69918 4.46632 2.97102 4.23502 4.77984 0.63388 4.68581 3.76781 4.05413 3.46306 2.04533 5.75329 4.56372 5 P - - -
+ 2.68616 4.42236 2.77530 2.73134 3.46365 2.40523 3.72505 3.29295 2.67751 2.69303 4.24634 2.90357 2.73739 3.18157 2.89783 2.37897 2.77530 2.98529 4.58488 3.61514
+ 0.09682 2.39494 6.81068 0.10162 2.33687 0.48576 0.95510
+ 5 2.95325 4.65976 3.57762 2.20709 3.14816 2.51487 3.41109 4.78902 2.65862 3.19599 4.41042 3.45032 3.44719 2.43205 2.26492 2.25400 2.23196 3.66828 4.80003 4.52485 7 e - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01246 6.08833 4.59386 0.61958 0.77255 0.48576 0.95510
+ 6 2.74215 5.97618 2.19482 2.69150 4.58171 2.33553 3.83525 3.28222 2.95080 3.32698 5.01691 1.45822 3.52462 2.79670 2.90942 3.13467 3.27956 4.36668 6.40902 3.92307 8 n - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00341 6.07928 6.80162 0.61958 0.77255 0.44282 1.02784
+ 7 3.32507 4.98102 3.78072 3.31043 2.85257 4.76439 5.09585 2.50332 4.69760 1.03851 3.36125 4.91001 2.73206 4.83820 4.72389 4.07376 3.83146 1.59790 5.60385 4.42704 9 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.03752 6.08833 3.36505 0.61958 0.77255 0.48576 0.95510
+ 8 3.15997 4.90658 3.35204 2.72775 4.53493 3.60960 2.65074 3.69535 2.11078 4.01384 4.99896 3.14668 4.61695 2.40643 2.34723 1.92358 2.03982 3.05153 6.39127 4.98082 10 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00349 6.05430 6.77664 0.61958 0.77255 0.35749 1.20207
+ 9 1.76295 3.98252 5.55061 4.93551 2.13202 3.39992 5.09294 2.14638 4.23898 2.23988 3.42109 4.92079 4.39252 3.70640 3.99349 3.50811 3.63432 1.47830 4.51148 4.41177 11 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 10 3.01387 4.98892 2.91217 2.42744 5.22342 4.00576 3.74074 2.67275 2.47618 2.92529 3.89570 3.36720 4.15809 3.26810 2.80854 1.81572 2.02040 2.77133 4.92415 4.31555 12 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 11 2.41247 5.98374 2.24093 2.04842 3.41543 2.59695 4.10033 4.81544 3.05501 4.28918 5.02429 2.22829 2.90635 3.12939 3.01921 2.37278 3.01194 3.02522 6.41619 3.66635 13 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.06784 6.08833 2.75947 0.61958 0.77255 0.48576 0.95510
+ 12 2.77725 4.36386 3.23435 2.92496 4.75140 4.31852 4.53101 1.91389 3.01135 2.51491 3.47932 2.97934 3.54432 2.88257 2.68923 3.07794 2.71169 1.80880 6.06849 4.75973 14 v - - E
+ 2.68623 4.42259 2.77533 2.73059 3.46323 2.40500 3.72529 3.29333 2.67757 2.69369 4.24724 2.90364 2.73744 3.18108 2.89835 2.37891 2.77531 2.98493 4.58511 3.61510
+ 0.22113 1.62346 6.74643 0.44471 1.02446 0.29166 1.37446
+ 13 3.17575 5.97994 3.10322 2.84738 5.32369 2.00173 4.43389 4.80873 3.01150 3.75019 4.42663 2.23751 4.64014 2.74467 2.85546 1.99984 1.67133 4.36987 5.08444 3.58488 18 t - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 14 2.14203 5.98483 2.53686 2.20884 5.33077 2.76253 3.61799 4.81737 2.91636 3.96256 5.02525 2.79307 2.44932 3.35978 3.34773 1.76758 2.51815 4.12754 4.53404 4.35768 19 s - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02274 6.08833 3.90154 0.61958 0.77255 0.48576 0.95510
+ 15 3.45984 5.96297 2.32904 2.98671 5.30486 3.14893 3.59992 3.68067 2.95954 4.26690 5.00447 2.01875 4.62814 3.51950 2.89162 1.97303 1.47565 3.87160 6.39755 3.59993 20 t - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00344 6.06904 6.79138 0.61958 0.77255 0.40302 1.10352
+ 16 2.82603 5.98256 2.96292 2.53617 4.39559 3.14388 4.09532 4.81336 2.59005 4.28779 5.02326 3.12547 4.63955 2.76620 3.03618 1.28432 2.14874 3.55065 4.82032 3.29405 21 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 17 2.29842 4.96481 5.56794 4.95172 2.45211 3.33868 4.31545 1.97312 4.73378 1.34355 2.88087 4.92903 5.12608 4.86259 4.73754 4.07438 3.55674 1.71344 5.58685 3.78328 22 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 18 2.99930 4.68496 3.44656 2.53427 3.92510 4.04338 3.13178 3.10095 3.07007 2.68343 3.58599 3.17010 4.15335 2.63450 2.71950 2.30083 2.03779 2.23518 4.92400 3.84991 23 t - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 19 3.61302 4.50726 5.99163 5.39935 2.74200 5.23506 5.61087 1.85210 5.20622 1.10188 3.56291 5.40353 5.56305 5.33364 5.22134 4.56441 3.85751 1.20867 6.05610 4.88933 24 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 20 2.90508 5.98486 3.37356 2.37027 5.33083 3.46854 3.40789 4.81743 2.65230 3.22177 4.17825 2.67373 4.63906 2.52648 2.39431 1.50547 2.16764 4.37598 5.01440 5.00552 25 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 21 5.54218 6.63564 6.83891 6.61797 2.57168 6.35073 5.30532 3.96643 6.37377 3.18917 5.26281 6.07009 4.35269 6.11992 6.21105 5.74680 5.75143 4.86346 0.24436 3.66807 26 W - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 22 3.10862 5.98423 2.61761 2.10221 4.46995 3.93009 3.84182 3.79843 2.19229 3.09373 4.47555 2.66452 4.06864 2.59255 2.99987 1.99073 2.05618 3.67318 6.41655 4.47364 27 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 23 2.05280 5.87614 3.77610 2.63103 5.17655 3.25143 3.55897 3.09279 2.68152 3.35866 4.92882 3.43937 1.44938 3.29932 2.98336 2.85751 2.78420 3.02863 4.43359 4.47040 28 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 24 2.65644 5.88726 3.37601 2.96202 5.19190 3.53629 4.46143 4.20046 2.87295 2.91429 4.93884 3.27084 1.07653 3.39095 3.69926 2.07705 3.29723 2.92337 6.34501 4.95985 29 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.32165 6.08833 1.29911 0.61958 0.77255 0.48576 0.95510
+ 25 2.44244 5.77880 2.64467 2.21733 3.20572 3.66340 3.27861 4.60939 2.17717 2.95495 4.81953 3.17778 2.62084 2.96028 2.64039 2.55818 2.51134 3.52175 6.21164 4.20060 30 k - - S
+ 2.68557 4.42278 2.77404 2.73101 3.46370 2.40555 3.72548 3.29364 2.67779 2.69337 4.24743 2.90378 2.73741 3.18051 2.89835 2.37928 2.77557 2.98526 4.58530 3.61392
+ 1.12909 0.74203 1.60680 0.24883 1.51281 1.67198 0.20810
+ 26 2.76497 5.64634 2.06362 2.44254 4.06108 3.91520 3.28362 3.73992 2.46695 3.95074 4.68755 2.93859 2.87257 2.71813 3.08100 2.16767 2.28242 3.00778 6.08028 4.00221 33 d - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00580 5.54941 6.27176 0.61958 0.77255 1.23854 0.34222
+ 27 2.94904 4.81418 2.88265 2.99332 4.83563 1.49306 3.87927 3.68299 2.59086 2.53757 4.07313 2.89409 2.92833 3.04624 2.88166 2.82744 3.22994 3.21444 4.18838 4.04981 34 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00508 5.68074 6.40309 0.61958 0.77255 0.20085 1.70396
+ 28 2.96588 5.95917 2.45759 2.65943 5.30490 1.91234 3.11781 3.44164 2.78003 4.01788 4.99965 2.12379 3.26764 2.84040 2.87160 2.26272 3.15721 3.84740 4.86821 3.64128 35 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00351 6.05095 6.77330 0.61958 0.77255 0.34864 1.22298
+ 29 2.45969 5.96445 2.88574 2.61716 5.30131 1.53630 4.43818 3.46883 2.98393 3.60366 4.33332 3.25719 4.28257 3.08417 2.40821 2.08539 3.20111 2.81105 6.40207 4.25093 36 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 30 2.71563 5.98438 2.50720 1.96228 5.33013 3.47246 3.38617 3.68065 2.34086 4.03521 4.36775 3.08029 1.87041 2.90329 3.33287 2.70645 2.77558 2.97286 6.41666 4.17777 37 p - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 31 3.04837 4.96747 2.67316 4.92527 2.42064 4.14655 5.09097 1.34551 4.71334 2.18068 3.34829 4.91585 3.31178 4.15082 4.72663 3.69906 3.53551 1.88881 3.93067 3.04034 38 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 32 2.89418 4.58676 2.12720 2.65970 3.99748 4.30700 4.50689 3.12934 2.75241 2.32504 4.34805 3.25317 4.69765 2.93544 2.97945 2.48570 1.85268 2.60501 5.05387 4.40931 39 t - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 33 3.05045 5.96458 3.15002 2.79713 4.16491 1.56242 3.20986 4.07540 2.34002 3.77648 3.66616 2.65073 4.64351 3.21500 2.62101 2.34442 2.98761 3.25677 5.04578 3.36446 40 g - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 34 4.72855 5.99332 6.32397 5.91516 1.75259 5.71064 3.47111 3.64093 3.68669 3.44300 5.13564 5.60513 6.03397 5.64902 5.63703 5.05114 4.95149 3.46344 3.97019 0.49348 41 Y - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 35 3.03913 5.98101 2.74983 1.95825 3.75604 3.98121 3.78677 3.48894 2.41418 2.89991 5.02189 2.66693 4.63989 2.65222 2.20113 2.26435 2.64729 3.16844 6.41420 3.93691 42 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 36 3.75576 5.90373 6.92143 6.48083 5.27028 6.48043 7.33031 1.16190 6.46559 1.72148 4.18143 6.65320 6.63807 6.70678 6.63399 5.94811 5.00240 0.82398 7.51298 6.31097 43 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.04904 6.08833 3.08806 0.61958 0.77255 0.48576 0.95510
+ 37 2.63429 4.71789 2.89387 2.04081 4.17861 4.22097 3.38514 2.92734 2.36124 3.26230 4.97143 3.69265 4.61418 2.27063 2.38238 2.70982 2.11937 3.37005 6.36711 3.73375 44 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00353 6.04282 6.76517 0.61958 0.77255 0.32899 1.27173
+ 38 3.00800 2.48193 5.53105 4.91728 2.98458 4.75707 4.15268 2.83469 3.12355 2.32451 4.08737 4.91198 5.12099 4.84273 3.46182 3.58557 3.26283 2.28912 2.64554 1.29971 45 y - - E
+ 2.68641 4.42053 2.77543 2.73091 3.46377 2.40536 3.72420 3.29377 2.67764 2.69378 4.24582 2.90336 2.73763 3.18113 2.89660 2.37910 2.77543 2.98542 4.58500 3.61526
+ 0.12278 2.16768 6.81068 0.54422 0.86820 0.48576 0.95510
+ 39 2.52553 4.02469 3.60093 2.65311 4.18239 3.63052 4.17989 3.44209 2.14970 3.12319 4.96260 3.43770 4.02454 2.12722 2.15391 2.32250 3.25888 3.40611 2.73453 3.57446 49 q - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02932 6.08833 3.62591 0.61958 0.77255 0.48576 0.95510
+ 40 2.85303 5.96779 2.74660 1.91867 5.31393 3.60453 3.59476 4.33679 2.36399 3.57280 3.62613 2.83996 2.06170 2.51716 3.24767 2.43993 2.61505 3.39964 6.39984 4.98824 50 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00347 6.06248 6.78482 0.61958 0.77255 0.67944 0.70705
+ 41 2.55267 3.11480 2.72137 2.31006 5.21613 3.67111 4.08491 3.18721 2.11932 2.73126 3.73119 3.72342 3.44703 2.78931 3.31632 2.60923 2.50487 2.33623 6.34948 4.95631 51 k - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.09789 6.06248 2.39773 0.61958 0.77255 0.38130 1.14877
+ 42 3.41114 5.92195 2.00739 2.51445 4.35946 1.85149 4.04885 4.75310 3.02073 3.41727 4.96259 1.88803 4.57836 2.81891 2.77402 2.53317 2.79169 3.60394 6.35459 4.48731 52 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00370 5.99676 6.71911 0.61958 0.77255 0.25112 1.50474
+ 43 2.89692 5.98568 2.39354 2.04021 5.33202 2.12548 3.27810 4.81889 2.36649 3.39071 4.58505 2.82477 4.63888 2.99231 3.02264 2.04514 2.45319 3.82791 6.41761 5.00590 53 e - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 44 3.10206 5.95088 3.50928 2.19657 4.70794 1.83640 4.44201 3.85177 2.81849 3.20653 3.64542 2.17673 2.82486 2.50236 3.67274 2.64718 2.71954 3.18909 6.39210 3.73228 54 g - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.08059 6.08833 2.58819 0.61958 0.77255 0.48576 0.95510
+ 45 2.83017 5.93388 2.31048 1.94273 5.28007 2.46456 3.60606 4.35357 2.35448 2.95362 4.97424 3.06816 3.41033 2.69285 2.84649 2.21743 2.98206 3.67978 4.23187 4.95426 55 e - - C
+ 2.68733 4.40831 2.77609 2.73043 3.46444 2.40393 3.72592 3.29278 2.67833 2.69426 4.24827 2.90407 2.73626 3.18024 2.89744 2.37952 2.77650 2.98614 4.58019 3.61570
+ 1.45631 0.90375 1.01651 1.51529 0.24813 0.96821 0.47765
+ 46 2.32839 5.42660 2.93163 2.28220 4.02543 3.04571 3.03894 3.22247 2.82753 3.21315 3.89864 3.49093 2.50859 3.14260 2.89921 2.69284 3.05772 2.38519 4.38264 3.20345 66 e - - G
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00571 5.56406 6.28641 0.61958 0.77255 0.18459 1.78051
+ 47 2.69465 3.91083 2.42967 2.34662 4.43247 3.13708 3.62175 3.49809 2.56727 2.84127 4.03266 3.52527 3.00745 3.22895 3.52756 2.46523 2.69768 3.11906 2.19019 4.92515 67 w - - C
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00353 6.04443 6.76678 0.61958 0.77255 0.33269 1.26228
+ 48 2.67627 5.86490 3.17099 3.22595 3.40616 4.27494 3.15476 3.07365 2.21494 2.78239 4.39426 2.30764 3.56160 2.19351 2.71433 2.94392 2.62330 2.55032 5.16850 4.37026 68 q - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 49 3.05871 5.98132 3.36643 1.71285 5.32569 3.90513 2.27648 4.25125 2.92072 4.28630 4.28595 2.90579 3.33969 2.79371 2.63337 2.42582 2.46361 2.81009 3.46671 3.72048 69 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 50 2.88323 4.65127 3.40086 2.73607 2.41972 3.62669 3.91044 2.52424 2.75640 2.37424 3.94274 3.64921 4.76561 2.38668 2.64750 3.03028 3.09193 2.27100 6.08057 3.03402 70 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 51 3.36533 5.95840 2.65995 2.86095 3.44584 4.25167 3.55888 2.90987 2.78397 3.33346 3.90493 2.03375 3.68901 2.80089 2.78508 2.11531 1.97302 3.15541 6.39763 4.99330 71 t - - E
+ 2.68571 4.42246 2.77540 2.73144 3.46375 2.40497 3.72515 3.29375 2.67742 2.69376 4.24711 2.90367 2.73710 3.18135 2.89822 2.37876 2.77540 2.98457 4.58498 3.61524
+ 0.06628 2.76409 6.81068 0.97562 0.47314 0.48576 0.95510
+ 52 2.38926 5.49703 3.09615 2.80044 4.68202 3.76562 4.62096 2.19958 3.33274 2.03099 4.11871 2.97731 4.26404 3.83080 2.89542 3.19964 2.84193 1.56133 6.03936 4.75239 75 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 53 2.79501 4.92737 2.35659 2.60299 4.06511 2.98090 3.88301 4.80087 2.44593 3.57653 5.01701 3.37711 1.76863 3.53250 3.23955 1.94419 2.68524 2.95506 6.41016 5.00121 76 p - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 54 2.44542 5.98316 3.18675 2.55065 5.32835 2.12386 4.43300 4.38419 2.38413 2.93654 5.02378 2.50193 2.49139 3.27226 2.05133 2.36069 3.70337 4.12664 4.32391 4.48343 77 r - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 55 2.77179 5.98329 2.50848 2.76644 5.32854 3.30269 3.08416 4.38434 3.16759 4.28865 5.02390 2.27915 2.67265 2.61285 3.32102 2.18277 1.82444 2.83013 6.41587 4.35727 78 t - - T
+ 2.68621 4.42251 2.77546 2.73149 3.46380 2.40468 3.72521 3.29380 2.67767 2.69252 4.24716 2.90344 2.73766 3.18134 2.89827 2.37913 2.77442 2.98545 4.58503 3.61529
+ 0.07130 2.69245 6.81068 1.11635 0.39671 0.48576 0.95510
+ 56 2.32530 5.97446 3.57954 1.89562 5.31575 4.24796 3.32554 3.73278 2.42253 2.98562 5.01611 3.71687 3.10116 2.71107 2.91871 2.60336 1.70360 3.15915 6.40941 5.00074 83 t - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.35248 6.08833 1.22151 0.61958 0.77255 0.48576 0.95510
+ 57 2.95924 5.72336 2.75932 2.63159 3.96190 3.29462 3.22449 3.40062 2.77057 3.18108 3.56769 2.46117 2.98702 3.05715 2.72729 2.56520 1.96589 3.52719 6.16591 2.96938 84 t - - S
+ 2.68622 4.42162 2.77539 2.73088 3.46349 2.40510 3.72514 3.29311 2.67761 2.69358 4.24710 2.90367 2.73759 3.18166 2.89753 2.37894 2.77488 2.98538 4.58497 3.61523
+ 0.23969 1.55321 6.46298 0.15973 1.91309 0.51157 0.91517
+ 58 2.78411 5.86726 3.65151 2.46190 3.55121 3.32277 3.71415 3.82816 2.87545 3.69015 4.27003 2.90512 3.60994 2.68731 2.37548 1.72361 1.95655 3.42914 6.30822 3.85760 87 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00384 5.96109 6.68344 0.61958 0.77255 0.21363 1.64843
+ 59 2.13080 3.38910 5.56698 4.95075 2.41578 4.20194 3.39215 2.83299 4.73282 2.14660 3.19234 4.92810 5.12527 4.86169 4.18461 4.07348 3.03808 1.63705 4.66089 1.78369 88 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 60 3.12543 5.93769 2.99354 2.53954 5.26303 4.25659 3.21054 2.85212 2.62935 2.82513 3.45830 2.90110 4.19559 2.80624 3.10357 2.88568 1.50190 2.67316 6.38237 3.93622 89 t - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 61 3.61965 4.99402 3.63828 4.95783 2.26826 4.79135 5.12555 1.86647 4.74679 1.34194 3.74460 4.94944 5.15281 3.10559 4.75989 3.74420 3.85186 1.42486 5.61987 4.44474 90 l - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 62 3.10387 5.98366 3.06368 2.31445 4.05906 3.57903 3.48488 4.81531 2.43543 4.01680 3.91148 2.67498 2.99920 2.70828 2.56621 2.14984 1.90367 3.06274 4.55677 4.37671 91 t - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 63 3.34220 5.98744 1.86090 2.69096 5.33359 1.40608 3.63608 4.82043 2.48624 4.29318 4.45099 1.96888 4.06897 3.19339 3.48838 2.73868 3.70514 4.37867 6.41942 4.25681 92 g - - S
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 64 5.18530 6.36522 4.58586 6.57578 3.53131 6.59442 6.84537 2.81242 6.44067 0.21363 3.54046 6.78308 6.53953 6.19263 6.31583 5.99910 5.37457 3.39834 6.73440 5.83217 93 L - - -
+ 2.68590 4.42227 2.77521 2.73125 3.46356 2.40515 3.72496 3.29356 2.67743 2.69357 4.24692 2.90349 2.73741 3.18148 2.89803 2.37889 2.77521 2.98520 4.58479 3.61505
+ 0.02033 3.96193 6.81068 0.31431 1.31041 0.48576 0.95510
+ 65 2.93361 5.98253 3.16620 2.07447 5.32745 3.84017 3.84639 3.52003 2.07989 2.71701 4.56317 3.05465 3.94228 2.39023 2.13660 2.81003 2.42767 2.98359 6.41531 3.87097 95 e - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 66 2.17452 5.85112 3.79178 2.44872 5.14174 4.27993 4.47388 4.59086 3.04069 4.13287 4.42378 3.36057 0.82761 3.31072 3.71538 3.13243 3.15654 3.97958 4.90439 4.38214 96 p - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 67 2.72531 5.97666 2.50761 2.79752 4.22378 1.29966 2.70734 4.80294 2.85170 4.02964 5.01805 2.59981 4.64085 3.32835 3.25617 2.51345 3.59137 3.91820 4.88800 2.97800 97 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 68 2.39925 4.86641 3.79312 2.74568 5.13568 4.27988 3.97435 3.95098 2.69562 3.65359 3.00813 3.38952 4.67180 3.12070 2.33490 2.43668 1.27713 2.90106 6.31421 4.93977 98 t - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 69 2.87821 5.98261 2.71299 2.05681 3.93787 3.36966 3.57296 3.81023 2.25993 3.03102 3.49917 2.39917 3.09415 2.62154 2.82818 2.67359 2.51409 3.67730 4.58228 5.00448 99 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 70 6.32206 7.09639 6.95855 7.01624 2.70399 6.62558 5.12529 5.84365 6.77161 4.03604 6.32463 4.32154 6.86163 6.30239 6.48747 6.05185 6.49899 5.81871 5.18730 0.14189 100 Y - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 71 3.06725 5.97020 3.56838 1.93769 4.23056 3.77167 3.39655 3.53252 2.56448 3.45405 4.47893 2.47898 4.64226 2.55695 2.74362 2.36648 2.01401 2.66399 6.40629 3.70776 101 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 72 3.19486 4.19171 5.58508 4.96942 1.44027 4.15574 5.11433 1.81297 4.75161 2.09873 3.37140 4.94615 5.14143 4.88008 4.75485 4.09123 3.83769 1.47173 5.60267 3.09551 102 f - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 73 3.18039 4.06436 3.15201 2.27681 5.32468 3.77041 3.95744 3.70705 2.23538 4.28548 4.11883 2.88564 4.63997 2.58030 1.70576 2.27707 2.39981 3.62914 4.03739 3.61343 103 r - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 74 3.76685 5.84337 6.79391 6.31497 3.84743 6.27452 6.95358 1.59565 6.25134 2.11498 4.30213 6.44619 6.46746 6.44080 6.36566 5.70153 4.90672 0.53161 7.20703 6.03175 104 V - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 75 2.31005 4.88319 3.40675 2.63903 3.58848 4.26911 3.49342 3.09105 2.39543 3.00463 4.93879 3.41670 4.66153 1.98639 2.22144 3.11070 2.61129 2.78609 6.34491 2.92043 105 q - - E
+ 2.68621 4.42228 2.77522 2.73126 3.46357 2.40516 3.72497 3.29357 2.67744 2.69312 4.24693 2.90350 2.73743 3.18149 2.89804 2.37890 2.77522 2.98521 4.58480 3.61506
+ 0.03738 3.58894 4.70319 0.25135 1.50394 0.48576 0.95510
+ 76 0.79499 5.17226 4.80437 3.93376 4.33120 3.17569 4.96596 3.30029 4.15773 2.86829 4.32533 4.52823 5.01384 4.41886 4.42465 2.28661 2.19420 2.76335 5.81537 4.60940 107 a - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00340 6.08033 6.80268 0.61958 0.77255 0.44741 1.01966
+ 77 2.84306 4.15407 4.98296 3.19564 3.23517 4.66606 3.67524 2.49603 3.23224 2.21212 3.84796 4.62630 5.03633 2.88555 2.43211 3.49088 3.22704 1.33993 5.67363 2.88123 108 v - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 78 3.27061 4.75060 2.81965 3.10410 5.31934 3.95942 3.99367 3.88107 2.62205 4.02823 5.01830 1.35628 3.08534 3.32913 3.08546 1.88067 2.21938 4.02145 6.41122 3.76470 109 n - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00992 6.08833 4.87890 0.61958 0.77255 0.48576 0.95510
+ 79 2.39836 4.69624 2.57939 2.56364 4.72011 1.55094 3.74815 4.26504 2.61409 4.28517 5.02018 2.82673 4.26340 2.69971 2.87382 2.73983 2.53993 3.07568 6.41202 5.00074 110 g - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00340 6.08180 6.80415 0.61958 0.77255 0.45398 1.00812
+ 80 2.22211 4.94595 2.69424 2.44928 4.84552 2.32005 3.06335 2.95704 2.33976 3.55821 4.09648 2.87488 4.09930 2.85656 2.97877 3.08279 3.07714 2.39346 6.40553 4.01548 111 a - - T
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.38398 6.08833 1.15015 0.61958 0.77255 0.48576 0.95510
+ 81 2.96920 5.43248 3.46409 2.76236 3.93019 1.02513 4.29951 4.07917 3.10833 3.39330 4.50784 3.40559 4.48149 3.45547 3.56956 2.50552 2.39680 3.76237 5.94228 3.01765 112 g - - E
+ 2.68652 4.42259 2.77488 2.73144 3.46170 2.40466 3.72529 3.29388 2.67703 2.69373 4.24724 2.90335 2.73774 3.18162 2.89801 2.37895 2.77529 2.98552 4.58511 3.61537
+ 0.29928 1.35852 6.43163 0.48724 0.95274 1.77816 0.18506
+ 82 2.84273 4.18992 3.05053 2.12883 3.36284 2.75189 4.25559 3.03507 2.66396 2.65563 4.59024 2.63081 3.84786 2.76844 3.19058 2.84597 2.82776 2.89016 3.06821 3.41272 117 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00494 5.70928 6.43163 0.61958 0.77255 1.56406 0.23482
+ 83 3.37920 5.61493 3.74277 3.20384 4.92800 1.01625 3.96683 4.35082 2.94708 2.91738 4.72998 3.71516 3.70329 3.52945 3.00683 1.61777 3.61882 4.00263 6.13360 4.80162 118 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00481 5.73459 6.45693 0.61958 0.77255 0.30535 1.33510
+ 84 2.58463 5.93784 3.04102 2.09605 4.57465 2.51630 3.24109 4.26208 2.60545 3.44607 3.62705 3.20484 1.89678 2.68661 2.74662 2.97880 3.02092 3.23569 6.37074 4.50367 119 p - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00361 6.02233 6.74467 0.61958 0.77255 0.28862 1.38348
+ 85 2.48488 5.72055 3.87501 1.97538 3.04853 3.48010 4.51877 3.51898 2.88839 2.73568 4.42660 3.64380 2.08811 3.48814 2.70856 2.40769 2.92982 4.05679 2.77386 3.43366 120 e - - B
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 86 3.03720 5.94099 3.75455 2.96917 5.26587 2.91682 3.66571 4.11840 2.98472 4.23738 4.98891 3.74380 4.66031 3.40955 3.12788 0.72443 2.46104 4.32115 6.38683 4.99111 121 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00227 6.08723 * 0.61958 0.77255 0.00000 *
+//
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
- assertEquals(sf.getDescription(), "AGT");
+ assertEquals(sf.getDescription(), "agC/agT");
sf = proteinFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 4);
import static org.testng.AssertJUnit.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.util.ArrayList;
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
// gaps are grey, residues white
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
av.setGlobalColourScheme(new ZappoColourScheme());
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
Color[] newColours = new Color[24];
SequenceGroup[] groups = new SequenceGroup[1];
groups[0] = sg;
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
// G in group specified as magenta in Zappo
{
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
- AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
// non-legacy colouring
ResidueColourFinder rcf = new OverviewResColourFinder();
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
- c);
+ assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
// non legacy colouring with colour scheme
rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
import static org.testng.AssertJUnit.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.gui.JvOptionPane;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
{
SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
av.setGlobalColourScheme(new ZappoColourScheme());
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
assertEquals(Color.white,
SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
// gap
AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
+ final AlignViewportI av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
Color[] newColours = new Color[24];
import static org.testng.Assert.assertTrue;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.AlignmentViewport;
import java.util.List;
String data = ">Seq/20-45\nABCDEFGHIJKLMNOPQRSTUVWXYS\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(data,
DataSourceType.PASTE);
- AlignViewport av = af.getViewport();
+ AlignmentViewport av = af.getViewport();
/*
* scale has minor ticks at 5, 15, 25, major at 10 and 20
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.FeatureRenderer;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
*/
public class FeatureColourFinderTest
{
- private AlignViewport av;
+ private AlignViewportI av;
private SequenceI seq;
// TODO more test cases; check if help documentation matches implementation
}
-
- // @formatter:on
/**
* Test for colour calculation when the consensus percentage ignores gapped
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HmmerGlobalBackgroundTest {
+
+ @Test(groups = "Functional")
+ public void testFindColour() throws MalformedURLException, IOException
+ {
+ HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ SequenceI hmmSeq = file.getSeqsAsArray()[0];
+ AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
+ al.setHmmConsensus(hmmSeq);
+ ColourSchemeI scheme = new HmmerGlobalBackground(al);
+
+ /*
+ * 'A' in column 1, node 2, match emission 2.77204
+ * e-2.77204 = 0.0625
+ * background frequency is 0.0826
+ * ratio is 0.757, log is negative, colour is Orange
+ */
+ Color actual = scheme.findColour('A', 1, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ // gap is white
+ actual = scheme.findColour('-', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour(' ', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour('.', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+
+ /*
+ * 'Y' in column 4, node 5, match emission 4.41426
+ * e-4.41426 = 0.0121
+ * background frequency is 0.0292
+ * ratio is 0.414, log is negative, colour is Orange
+ */
+ actual = scheme.findColour('Y', 4, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ /*
+ * 'M' in column 109, no matching node, colour is reddish
+ */
+ actual = scheme.findColour('M', 109, null, null, 0);
+ assertEquals(actual, new Color(230, 0, 0));
+
+ /*
+ * 'I' in column 6, node 7, match emission 1.33015
+ * e-1.33015 = 0.2644
+ * background frequency is 0.0593
+ * ratio is 4.459, log is 1.495
+ * colour is graduated 1.495/4.52 or 84/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('I', 6, null, null, 0);
+ assertEquals(actual, new Color(171, 171, 255));
+
+ /*
+ * 'V' in column 14, node 15, match emission 0.44769
+ * e-0.44769 = 0.6391
+ * background frequency is 0.0686
+ * ratio is 9.316, log is 2.232
+ * colour is graduated 2.232/4.52 or 126/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('V', 14, null, null, 0);
+ assertEquals(actual, new Color(129, 129, 255));
+
+ /*
+ * invalid symbol is White
+ */
+ actual = scheme.findColour('X', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ }
+
+}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HmmerLocalBackgroundTest {
+
+ @Test(groups = "Functional")
+ public void testFindColour() throws MalformedURLException, IOException
+ {
+ HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ /*
+ * alignment with 20 residues and background frequencies:
+ * A/a, S 3/20 = 0.15
+ * M, K 4/20 = 0.2
+ * V 2/20 = 0.1
+ * Q, R, L 1/20 = 0.05
+ * log(totalCount) = log(20) = 2.996
+ */
+ SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
+ SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
+ SequenceI hmmSeq = file.getSeqsAsArray()[0];
+ AnnotatedCollectionI ac = new Alignment(
+ new SequenceI[]
+ { hmmSeq, seq1, seq2 });
+ ac.setHmmConsensus(hmmSeq);
+ ColourSchemeI scheme = new HmmerLocalBackground(ac);
+
+ /*
+ * 'A' in column 1, node 2, match emission 2.77204
+ * e-2.77204 = 0.0625
+ * background frequency is 0.15
+ * ratio is < 1, log is negative, colour is Orange
+ */
+ Color actual = scheme.findColour('A', 1, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ // gap is white
+ actual = scheme.findColour('-', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour(' ', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour('.', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+
+ /*
+ * 'L' in column 3, node 4, match emission 1.98342
+ * e-1.98342 = 0.1376
+ * background frequency is 0.05
+ * ratio is 2.752, log is 1.012
+ * colour is graduated 1.012/2.996 or 86/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('L', 3, null, null, 0);
+ assertEquals(actual, new Color(169, 169, 255));
+
+ /*
+ * invalid symbol is White
+ */
+ actual = scheme.findColour('X', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ }
+
+}
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
*/
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
- AlignViewport viewport = af.getViewport();
+ AlignmentViewport viewport = af.getViewport();
viewport.setIgnoreGapsConsensus(false, af.alignPanel);
while (viewport.getConsensusSeq() == null)
{
*/
package jalview.structure;
+import static org.junit.Assert.assertArrayEquals;
+import static org.testng.Assert.assertNotNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolCommands;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceRenderer;
+import jalview.gui.StructureChooser;
import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.io.Jalview2xmlBase;
import jalview.io.StructureFile;
import jalview.util.MapList;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
import java.util.ArrayList;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-public class StructureSelectionManagerTest
+@Test(singleThreaded = true)
+public class StructureSelectionManagerTest extends Jalview2xmlBase
{
+ @Override
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertEquals("1gaq", sf.getFeatureGroup());
assertEquals("ALA: 1 1gaqB", sf.getDescription());
}
+
+ /**
+ * Verify that RESNUM sequence features are present after creating a PDB
+ * mapping from a local file, then that everything stays in the same place
+ * when the file is viewed. The corner case is that 4IM2 is a fragment of a
+ * PDB file, which still includes the 'ID' field - a bug in Jalview 2.10.3
+ * causes features, annotation and positions to be remapped to the wrong place
+ * on viewing the structure
+ */
+ @Test(groups = { "Network" })
+ public void testMapping_EqualsFeatures()
+ {
+ // for some reason 'BeforeMethod' (which should be inherited from
+ // Jalview2XmlBase isn't always called)...
+ Desktop.instance.closeAll_actionPerformed(null);
+ try {
+ Thread.sleep(200);
+ } catch (Exception foo) {};
+ SequenceI seq = new Sequence("4IM2|A",
+ "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
+ String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
+ StructureSelectionManager sm = new StructureSelectionManager();
+ sm.setProcessSecondaryStructure(true);
+ sm.setAddTempFacAnnot(true);
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[]
+ { null }, P4IM2_MISSING,
+ DataSourceType.FILE);
+ assertTrue(pmap != null);
+
+ assertEquals(1, pmap.getSeqs().size());
+ assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
+
+ List<int[]> structuremap1 = new ArrayList(
+ sm.getMapping(P4IM2_MISSING)[0]
+ .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
+
+ /*
+ * Verify a RESNUM sequence feature in the PDBfile sequence
+ * LEU468 - start+0
+ * VAL479 - start+11
+ * MET486 - start+12
+ * GLY496 - start+13
+ * GLU516 - start+33 (last)
+ *
+ * Expect features and mapping to resolve to same residues.
+ * Also try creating a view and test again
+ *
+ */
+ String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET",
+ "486", "GLY", "496", "GLU", "516" };
+ int[] offset = new int[] { 0, 11, 12, 13, 33 };
+
+ List<String> fdesc = new ArrayList<>();
+ for (int f = 0; f < feats.length; f += 2)
+ {
+ fdesc.add(feats[f] + ": " + feats[f + 1] + " 4im2A");
+ }
+ SequenceI pdbseq = pmap.getSeqs().get(0);
+ verifySeqFeats(pdbseq, offset, fdesc);
+
+ /// Now load as a view
+
+ AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/4IM2_missing.pdb", DataSourceType.FILE);
+ Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800,
+ 400);
+ AlignmentI pdbal = alf.getViewport().getAlignment();
+ SequenceI pdb_viewseq = pdbal.getSequenceAt(0);
+ assertEquals(pdb_viewseq.getSequenceAsString(),
+ seq.getSequenceAsString());
+ // verify the feature location on the sequence when pdb imported as an
+ // alignment
+ verifySeqFeats(pdb_viewseq, offset, fdesc);
+
+
+ JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
+ pdb_viewseq, "4IM2");
+
+ // and check all is good with feature location still
+ verifySeqFeats(pdb_viewseq, offset, fdesc);
+
+ // finally check positional mapping for sequence and structure
+ PDBEntry pdbe = seq.getPDBEntry("4IM2");
+ StructureSelectionManager apssm = alf.alignPanel
+ .getStructureSelectionManager();
+ StructureMapping[] smap = apssm
+ .getMapping(pdbe.getFile());
+ assertNotNull(smap);
+ assertNotNull(smap[0]);
+ // find the last position in the alignment sequence - this is not
+ // 'SequenceI.getEnd()' - which gets the last PDBRESNUM rather than
+ // SequenceI.getStart() + number of residues in file...
+ int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength());
+ List<int[]> ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(),
+ realSeqEnd);
+ assertEquals(structuremap1.size(), ranges.size());
+ int tot_mapped = 0;
+ for (int p = 0; p < ranges.size(); p++)
+ {
+ assertArrayEquals(structuremap1.get(p), ranges.get(p));
+ tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]);
+ }
+
+ assertEquals(pdb_viewseq.getLength(), tot_mapped);
+
+ int lastmappedp = StructureMapping.UNASSIGNED_VALUE;
+ for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq
+ .findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++)
+ {
+ int mappedp = smap[0].getPDBResNum(rp);
+ if (mappedp != StructureMapping.UNASSIGNED_VALUE)
+ {
+ tot_mapped--;
+ if (lastmappedp == mappedp)
+ {
+ Assert.fail("Duplicate mapped position at " + rp + " (dupe = "
+ + mappedp + ")");
+ }
+ }
+ }
+
+ Assert.assertEquals(tot_mapped, 0,
+ "Different number of mapped residues compared to ranges of mapped residues");
+
+ // positional mapping to atoms for color by structure is still wrong, even
+ // though panel looks correct.
+
+ StructureMappingcommandSet smcr[] = JmolCommands
+ .getColourBySequenceCommand(apssm,
+ new String[]
+ { pdbe.getFile() },
+ new SequenceI[][]
+ { new SequenceI[] { pdb_viewseq } },
+ new SequenceRenderer(alf.alignPanel.getAlignViewport()),
+ alf.alignPanel);
+ // Expected - all residues are white
+ for (StructureMappingcommandSet smm : smcr)
+ {
+ for (String c : smm.commands)
+ {
+ System.out.println(c);
+ }
+ }
+ }
+
+ private void verifySeqFeats(SequenceI pdbseq, int[] offset,
+ List<String> fdesc)
+ {
+ for (int o = 0; o < offset.length; o++)
+ {
+ int res = pdbseq.findPosition(offset[o]);
+ List<SequenceFeature> sf = pdbseq.getFeatures().findFeatures(res, res,
+ "RESNUM");
+ assertEquals("Expected sequence feature at position " + res + "("
+ + offset[o] + ")", 1, sf.size());
+ assertEquals("Wrong description at " + res + "(" + offset[o] + ")",
+ fdesc.get(o), sf.get(0).getDescription());
+ }
+
+ }
+
+ @Test(groups = { "Network" })
+ public void testAssociatedMappingToSubSeq() throws Exception
+ {
+
+ // currently this test fails if trimming is enabled
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
+ Boolean.FALSE.toString());
+ String TEMP_FACTOR_AA="Temperature Factor";
+ String PDBID = "4IM2";
+ String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
+ "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" +
+ "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" +
+ "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" +
+ "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" +
+ "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" +
+ "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" +
+ "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" +
+ "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" +
+ "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" +
+ "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" +
+ "GGLRNVDCL";
+ /*
+ * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
+ *
+ * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
+ */
+ String FullLengthAnnot = "JALVIEW_ANNOTATION\n" +
+ "# Created: Mon Feb 05 15:30:20 GMT 2018\n" +
+ "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" +
+ "\n" +
+ "\n" +
+ "SEQUENCE_REF\tTBK1_HUMAN\n"
+ + "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
+ +
+ "\n" +
+ "";
+ AlignFrame alf_full=new
+ FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
+ alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
+ AlignmentI al_full = alf_full.getViewport().getAlignment();
+ AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
+ .next();
+ assertNotNull(fullseq_tf);
+
+ // getMappingFor
+ // AlignmentI al_full=alf_full.getViewport().getAlignment();
+ //
+ // // load 4IM2 (full length, SIFTS onto full alingnment)
+ // SiftsSettings.setMapWithSifts(true);
+ // StructureChooser schoose = new StructureChooser(selectedSeqs_full,
+ // seq_full,
+ // alf_full.getViewport().getAlignPanel());
+ // schoose.selectStructure(PDBID);
+ // schoose.ok_ActionPerformed();
+
+ AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+ ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
+ DataSourceType.PASTE);
+ Desktop.addInternalFrame(alf, "Foo", 800, 600);
+ ;
+ AlignmentI al = alf.getViewport().getAlignment();
+ SequenceI seq = al.getSequenceAt(0);
+ assertEquals(470, seq.getStart());
+ // load 4IM2 (full length, SIFTS)
+ SiftsSettings.setMapWithSifts(true);
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
+ PDBID);
+
+ AlignmentAnnotation subseq_tf=null;
+ assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
+
+ if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
+ {
+ // FIXME JAL-2321 - don't see reference annotation on alignment the first
+ // time
+ // around
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+
+ if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
+ .hasNext())
+ {
+ Assert.fail(
+ "JAL-2321 or worse has occured. No secondary structure added to alignment.");
+ }
+ }
+ subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
+ .next();
+ // verify against annotation after loading 4IM2 to full length TBK1_HUMAN
+ // verify location of mapped residues
+ // verify location of secondary structure annotation
+ // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
+ // GLU497 (helix),
+
+ // check there is or is not a tempfactor for each mapped position, and that
+ // values are equal for those positions.
+ for (int p=seq.getStart();p<=seq.getEnd();p++)
+ {
+ Annotation orig,subseq;
+ orig = fullseq_tf.getAnnotationForPosition(p);
+ subseq = subseq_tf.getAnnotationForPosition(p);
+ if (orig == null)
+ {
+ Assert.assertNull(subseq,
+ "Expected no annotation transferred at position " + p);
+ }
+ ;
+ if (orig != null)
+ {
+ Assert.assertNotNull(subseq,
+ "Expected annotation transfer at position " + p);
+ assertEquals(orig.value, subseq.value);
+ }
+ ;
+
+ }
+ }
+
+ private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
+ SequenceI seq,
+ String pDBID)
+ {
+
+ SequenceI[] selectedSeqs = new SequenceI[] { seq };
+
+ StructureChooser schoose = new StructureChooser(selectedSeqs, seq,
+ alf.getViewport().getAlignPanel());
+
+ try
+ {
+ Thread.sleep(5000);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ Assert.assertTrue(schoose.selectStructure(pDBID),
+ "Couldn't select structure via structure chooser: " + pDBID);
+ schoose.showStructures(true);
+ return schoose.getOpenedStructureViewer();
+ }
+
}
--- /dev/null
+1.8, 4.53
+3.4, 2.65
+0, 5.4
+6.4, 10.8
\ No newline at end of file
--- /dev/null
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMProbabilityDistributionAnalyserTest {
+
+ HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+ @Test
+ public void testMoveToFile() throws IOException
+ {
+
+ BufferedReader br = new BufferedReader(new FileReader(
+ "test/jalview/util/test_Fams_for_probability_analysis"));
+ analyser.moveLocationBy(1, br);
+
+ String line = br.readLine();
+ assertEquals(line, "# STOCKHOLM 1.0");
+ line = br.readLine();
+ assertEquals(line, "seq1 ATW");
+ line = br.readLine();
+ assertEquals(line, "seq2 ATI");
+
+ }
+
+ @Test
+ public void testCountValidResidues()
+ {
+ analyser.sequences = new Vector<>();
+ analyser.hmm = new HiddenMarkovModel();
+ analyser.hmm.setProperty("LENG", "8");
+
+ List<HMMNode> nodes = new ArrayList<>();
+ nodes.add(new HMMNode());
+ for (int i = 1; i < 9; i++)
+ {
+ HMMNode node = new HMMNode();
+ node.setResidueNumber(i - 1);
+ nodes.add(node);
+
+ }
+ PA.setValue(analyser.hmm, "nodes", nodes);
+
+ SequenceI[] sequence = new Sequence[] {
+ new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
+ new Sequence("seq3", "--.ATccGc") };
+ analyser.sequences.add(sequence[0]);
+ analyser.sequences.add(sequence[1]);
+ analyser.sequences.add(sequence[2]);
+
+ int count = analyser.countValidResidues();
+ assertEquals(count, 16);
+ }
+
+ @Test(priority = 0)
+ public void testReadBinned() throws IOException
+ {
+ analyser.readBinned("test/jalview/util/");
+ Map<String, Double> map = analyser.binned;
+ assertEquals(map.get("1.8"), 4.53);
+ assertEquals(map.get("3.4"), 2.65);
+ assertEquals(map.get("6.4"), 10.8);
+ assertEquals(map.get("0"), 5.4);
+ }
+
+ @Test
+ public void testReadRaw() throws IOException
+ {
+ analyser.readRaw("test/jalview/util/");
+ List<ArrayList<Double>> list = analyser.raw;
+
+ assertEquals(list.get(0).get(0), 1.43);
+ assertNull(list.get(0).get(2));
+ assertEquals(list.get(1).get(1), 1.2);
+ assertEquals(list.get(2).get(0), 5.6);
+ assertEquals(list.get(2).get(2), 6.8);
+
+ }
+
+ @Test(priority = 1)
+ public void testProcessData() throws IOException
+ {
+ analyser.keepRaw = true;
+ BufferedReader brFam = new BufferedReader(new FileReader(
+ "test/jalview/util/test_Fams_for_probability_analysis"));
+ BufferedReader brHMM = new BufferedReader(new FileReader(
+ "test/jalview/util/test_HMMs_for_probability_analysis"));
+ analyser.readStockholm(brFam);
+ analyser.readHMM(brHMM);
+ analyser.processData(6);
+ Map<String, Double> map = analyser.binned;
+ List<ArrayList<Double>> list = analyser.raw;
+ assertEquals(map.get("1.8"), 4.863, 0.001d);
+ assertEquals(map.get("3.4"), 2.65);
+ assertEquals(map.get("0"), 5.4);
+ assertEquals(map.get("6.4"), 10.8);
+ assertEquals(map.get("1.4"), 0.166667, 0.00001d);
+ assertEquals(map.get("4.4"), 0.5);
+
+ }
+}
assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
}
- @Test(groups = "Functional")
- public void testAddRange()
- {
- int[] range = { 1, 5 };
- List<int[]> ranges = new ArrayList<>();
-
- // add to empty list:
- MapList.addRange(range, ranges);
- assertEquals(1, ranges.size());
- assertSame(range, ranges.get(0));
-
- // extend contiguous (same position):
- MapList.addRange(new int[] { 5, 10 }, ranges);
- assertEquals(1, ranges.size());
- assertEquals(1, ranges.get(0)[0]);
- assertEquals(10, ranges.get(0)[1]);
-
- // extend contiguous (next position):
- MapList.addRange(new int[] { 11, 15 }, ranges);
- assertEquals(1, ranges.size());
- assertEquals(1, ranges.get(0)[0]);
- assertEquals(15, ranges.get(0)[1]);
-
- // change direction: range is not merged:
- MapList.addRange(new int[] { 16, 10 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(10, ranges.get(1)[1]);
-
- // extend reverse contiguous (same position):
- MapList.addRange(new int[] { 10, 8 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(8, ranges.get(1)[1]);
-
- // extend reverse contiguous (next position):
- MapList.addRange(new int[] { 7, 6 }, ranges);
- assertEquals(2, ranges.size());
- assertEquals(16, ranges.get(1)[0]);
- assertEquals(6, ranges.get(1)[1]);
-
- // change direction: range is not merged:
- MapList.addRange(new int[] { 6, 9 }, ranges);
- assertEquals(3, ranges.size());
- assertEquals(6, ranges.get(2)[0]);
- assertEquals(9, ranges.get(2)[1]);
-
- // not contiguous: not merged
- MapList.addRange(new int[] { 11, 12 }, ranges);
- assertEquals(4, ranges.size());
- assertEquals(11, ranges.get(3)[0]);
- assertEquals(12, ranges.get(3)[1]);
- }
-
/**
* Check state after construction
*/
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Iterator;
import java.util.List;
import org.testng.annotations.BeforeClass;
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[]", dnaSelection.getSelected().toString());
- List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+ Iterator<int[]> regions = dnaHidden.iterator();
+ assertEquals(1, dnaHidden.getNumberOfRegions());
+ assertEquals("[0, 4]", Arrays.toString(regions.next()));
/*
* Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
proteinSelection.hideSelectedColumns(1, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- hidden = dnaHidden.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+ regions = dnaHidden.iterator();
+ assertEquals(1, dnaHidden.getNumberOfRegions());
+ assertEquals("[0, 3]", Arrays.toString(regions.next()));
/*
* Column 2 in protein picks up gaps only - no mapping
proteinSelection.hideSelectedColumns(2, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
+ assertEquals(0, dnaHidden.getNumberOfRegions());
/*
* Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
- hidden = dnaHidden.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+ regions = dnaHidden.iterator();
+ assertEquals(1, dnaHidden.getNumberOfRegions());
+ assertEquals("[5, 10]", Arrays.toString(regions.next()));
/*
* Combine hiding columns 1 and 3 to get discontiguous hidden columns
proteinSelection.hideSelectedColumns(3, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- hidden = dnaHidden.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
- assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+ regions = dnaHidden.iterator();
+ assertEquals(2, dnaHidden.getNumberOfRegions());
+ assertEquals("[0, 3]", Arrays.toString(regions.next()));
+ assertEquals("[5, 10]", Arrays.toString(regions.next()));
}
@Test(groups = { "Functional" })
assertEquals(1, ranges.size());
assertEquals(9, ranges.get(0)[1]);
}
+
+ @Test(groups = "Functional")
+ public void testAddRange()
+ {
+ int[] range = { 1, 5 };
+ List<int[]> ranges = new ArrayList<>();
+
+ // add to empty list:
+ MappingUtils.addRange(range, ranges);
+ assertEquals(1, ranges.size());
+ assertSame(range, ranges.get(0));
+
+ // extend contiguous (same position):
+ MappingUtils.addRange(new int[] { 5, 10 }, ranges);
+ assertEquals(1, ranges.size());
+ assertEquals(1, ranges.get(0)[0]);
+ assertEquals(10, ranges.get(0)[1]);
+
+ // extend contiguous (next position):
+ MappingUtils.addRange(new int[] { 11, 15 }, ranges);
+ assertEquals(1, ranges.size());
+ assertEquals(1, ranges.get(0)[0]);
+ assertEquals(15, ranges.get(0)[1]);
+
+ // change direction: range is not merged:
+ MappingUtils.addRange(new int[] { 16, 10 }, ranges);
+ assertEquals(2, ranges.size());
+ assertEquals(16, ranges.get(1)[0]);
+ assertEquals(10, ranges.get(1)[1]);
+
+ // extend reverse contiguous (same position):
+ MappingUtils.addRange(new int[] { 10, 8 }, ranges);
+ assertEquals(2, ranges.size());
+ assertEquals(16, ranges.get(1)[0]);
+ assertEquals(8, ranges.get(1)[1]);
+
+ // extend reverse contiguous (next position):
+ MappingUtils.addRange(new int[] { 7, 6 }, ranges);
+ assertEquals(2, ranges.size());
+ assertEquals(16, ranges.get(1)[0]);
+ assertEquals(6, ranges.get(1)[1]);
+
+ // change direction: range is not merged:
+ MappingUtils.addRange(new int[] { 6, 9 }, ranges);
+ assertEquals(3, ranges.size());
+ assertEquals(6, ranges.get(2)[0]);
+ assertEquals(9, ranges.get(2)[1]);
+
+ // not contiguous: not merged
+ MappingUtils.addRange(new int[] { 11, 12 }, ranges);
+ assertEquals(4, ranges.size());
+ assertEquals(11, ranges.get(3)[0]);
+ assertEquals(12, ranges.get(3)[1]);
+ }
}
--- /dev/null
+Seq1, Seq2, Seq3
+1.43, 2.34, 5.6,
+EMPTY, 1.2, 0.05,
+EMPTY, 5.4, 6.8,
\ No newline at end of file
--- /dev/null
+# STOCKHOLM 1.0
+seq1 AW
+seq2 GW
+seq3 AW
+//
+# STOCKHOLM 1.0
+seq1 ATW
+seq2 ATI
+//
+# STOCKHOLM 1.0
+seq1 R-WW
+seq2 RAWW
+//
\ No newline at end of file
--- /dev/null
+HMMER3/f [3.1b2 | February 2015]
+NAME test1
+LENG 4
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:35:06 2017
+NSEQ 3
+EFFN 3.000000
+CKSUM 657102310
+STATS LOCAL MSV -5.0223 0.82341
+STATS LOCAL VITERBI -4.9569 0.82341
+STATS LOCAL FORWARD -2.0282 0.82341
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.94296 5.20658 4.78882 4.52987 4.66525 2.54188 5.19553 2.25221 4.08549 3.87133 5.00250 4.55734 4.73106 4.65220 2.77287 3.67799 1.53923 3.75384 1.48526 4.84023
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.00000 *
+ 1 0.67027 4.79120 4.60974 4.51892 5.43734 1.28080 5.43621 4.90028 4.64310 4.61059 5.39837 4.28688 4.41468 4.80804 4.79047 3.08135 3.44468 4.10506 6.74908 5.67939 1 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 2 5.43405 6.34487 5.85697 5.84679 4.39288 5.10370 5.65594 5.70664 5.69821 4.87848 6.25251 5.89664 5.70261 6.00722 5.60902 5.64576 5.80049 5.59366 0.08910 4.36301 2 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 3 3.42384 5.23617 4.84601 4.77568 5.39247 4.01365 5.64153 4.72950 4.75585 4.52264 5.55782 4.69647 4.81267 5.08969 4.87301 3.64217 0.20934 4.25217 6.65833 5.63018 3 T - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 4 3.53954 5.09963 4.71395 4.06038 4.20429 4.44020 4.65482 0.90152 3.16536 2.96072 4.13056 4.31689 4.83725 3.95143 1.46549 3.86829 3.78084 2.85654 5.74911 4.54685 4 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00730 4.92341 * 0.61958 0.77255 0.00000 *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME test2
+LENG 3
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:36:50 2017
+NSEQ 2
+EFFN 2.000000
+CKSUM 777554360
+STATS LOCAL MSV -5.2452 0.95763
+STATS LOCAL VITERBI -5.2886 0.95763
+STATS LOCAL FORWARD -1.5134 0.95763
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.33364 4.79082 4.44132 4.24796 3.91456 3.75718 4.85762 2.23342 4.16821 3.09137 4.29744 4.25088 4.41741 4.46803 4.31080 3.33397 1.39376 3.21010 2.54819 4.14914
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.00000 *
+ 1 0.32372 4.76536 4.42980 4.32857 5.00499 3.55951 5.22620 4.27004 4.37081 4.10495 5.08789 4.22499 4.36948 4.63911 4.51684 3.12947 3.46009 3.76842 6.33337 5.25783 1 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 2 3.04414 4.87155 4.35068 4.21532 4.89213 3.66881 5.13994 4.14202 4.17893 3.96810 5.00600 4.23490 4.44590 4.53729 4.35178 3.25814 0.35496 3.73038 6.23308 5.12388 2 T - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 3 3.41901 4.77187 4.98694 4.49106 3.10447 4.49364 4.52024 1.21391 4.22709 2.30875 3.57865 4.53952 4.83367 4.43564 4.31127 3.88439 3.66452 2.61326 1.44329 3.34125 3 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 4.62006 * 0.61958 0.77255 0.00000 *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME test3
+LENG 4
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:37:01 2017
+NSEQ 2
+EFFN 2.000000
+CKSUM 986955970
+STATS LOCAL MSV -5.4578 0.80004
+STATS LOCAL VITERBI -5.2499 0.80004
+STATS LOCAL FORWARD -2.1856 0.80004
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.16700 5.33023 4.57707 4.32329 4.15728 4.03215 4.83242 4.49728 3.73978 4.00181 5.18156 4.45520 4.63709 4.41734 1.53081 3.84281 4.10073 4.20172 0.82417 4.15750
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.00000 *
+ 1 4.09153 5.75008 4.67229 4.09411 5.31638 4.34678 4.67762 4.97541 2.93879 4.35023 5.37643 4.37234 4.85576 3.90366 0.27042 4.17197 4.33362 4.67489 6.11461 5.14175 1 R - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.39762 4.62483 1.14482 0.61958 0.77255 0.48576 0.95510
+ 2 0.58385 4.42717 3.89187 3.72118 4.47383 3.23815 4.69159 3.65968 3.74862 3.52210 4.52478 3.76053 4.01438 4.05655 3.96007 2.78076 3.08518 3.24526 5.86063 4.71068 2 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02145 4.24866 4.97100 0.61958 0.77255 0.27360 1.42978
+ 3 4.82318 5.87391 5.36844 5.28961 3.81117 4.70308 5.10523 4.98084 5.06729 4.21822 5.56037 5.33222 5.28501 5.40387 5.04111 5.02415 5.17266 4.88017 0.16601 3.78547 3 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 4 4.82318 5.87391 5.36844 5.28961 3.81117 4.70308 5.10523 4.98084 5.06729 4.21822 5.56037 5.33222 5.28501 5.40387 5.04111 5.02415 5.17266 4.88017 0.16601 3.78547 4 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 4.62006 * 0.61958 0.77255 0.00000 *
+//
\ No newline at end of file
*/
package jalview.ws;
+import static org.testng.Assert.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
+import java.util.Arrays;
import java.util.List;
+import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
testRetrieveProteinSeqFromPDB();
}
+ private class TestRetrieveObject
+ {
+ String id;
+
+ int expectedHeight;
+
+ public TestRetrieveObject(String id, int expectedHeight)
+ {
+ super();
+ this.id = id;
+ this.expectedHeight = expectedHeight;
+ }
+
+ }
+
+ private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+ new TestRetrieveObject("1QIP", 4),
+ new TestRetrieveObject("4IM2", 1));
+
private void testRetrieveProteinSeqFromPDB() throws Exception
{
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
- AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
- assertTrue(response != null);
- assertTrue(response.getHeight() == 4);
- for (SequenceI sq : response.getSequences())
+ StringBuilder errors = new StringBuilder();
+ for (TestRetrieveObject str : toRetrieve)
{
- assertTrue("No annotation transfered to sequence.",
- sq.getAnnotation().length > 0);
- assertTrue("No PDBEntry on sequence.",
- sq.getAllPDBEntries().size() > 0);
- org.testng.Assert
- .assertEquals(sq.getEnd() - sq.getStart() + 1,
- sq.getLength(),
- "Sequence start/end doesn't match number of residues in sequence");
+ AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+ assertTrue("No aligment for " + str.id, response != null);
+ assertEquals(response.getHeight(), str.expectedHeight,
+ "Number of chains for " + str.id);
+ for (SequenceI sq : response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence " + sq.getName(),
+ sq.getAnnotation().length > 0);
+ assertTrue("No PDBEntry on sequence " + sq.getName(),
+ sq.getAllPDBEntries().size() > 0);
+ // FIXME: should test that all residues extracted as sequences from
+ // chains in structure have a mapping to data in the structure
+ List<SequenceFeature> prev = null;
+ int lastp = -1;
+ for (int col = 1; col <= sq.getLength(); col++)
+ {
+ List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
+ if (sf.size() != 1)
+ {
+ errors.append(
+ str.id + ": " +
+ "Expected one feature at column (position): "
+ + (col - 1)
+ + " (" + sq.findPosition(col - 1) + ")"
+ + ": saw "
+ + sf.size());
+ errors.append("\n");
+ if (prev != null)
+ {
+ errors.append("Last Feature was at position " + lastp + ": "
+ + prev.get(0).toString());
+ errors.append("\n");
+ }
+ }
+ else
+ {
+ prev = sf;
+ lastp = sq.findPosition(col - 1);
+ }
+ }
+ }
+ }
+ if (errors.length() > 0)
+ {
+ Assert.fail(errors.toString());
}
}
-
}
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class PfamFullTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetURL()
+ {
+ String path = "pfam.xfam.org/family/ABC/alignment/full";
+
+ // with default value for domain
+ String url = new PfamFull().getURL(" abc ");
+ assertEquals(url, "https://" + path);
+
+ // with override in properties
+ Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+ url = new PfamFull().getURL(" abc ");
+ assertEquals(url, "http://" + path);
+ }
+}
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class PfamSeedTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetURL()
+ {
+ String path = "pfam.xfam.org/family/ABC/alignment/seed";
+
+ // with default value for domain
+ String url = new PfamSeed().getURL(" abc ");
+ assertEquals(url, "https://" + path);
+
+ // with override in properties
+ Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+ url = new PfamSeed().getURL(" abc ");
+ assertEquals(url, "http://" + path);
+ }
+}
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class RfamFullTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetURL()
+ {
+ String path = "rfam.xfam.org/family/ABC/alignment/full";
+
+ // with default value for domain
+ String url = new RfamFull().getURL(" abc ");
+ assertEquals(url, "https://" + path);
+
+ // with override in properties
+ Cache.setProperty(Rfam.RFAM_BASEURL_KEY, "http://rfam.xfam.org");
+ url = new RfamFull().getURL(" abc ");
+ assertEquals(url, "http://" + path);
+ }
+}
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class RfamSeedTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetURL()
+ {
+ String path = "rfam.xfam.org/family/ABC/alignment/stockholm";
+
+ // with default value for domain
+ String url = new RfamSeed().getURL(" abc ");
+ assertEquals(url, "https://" + path);
+
+ // with override in properties
+ Cache.setProperty(Rfam.RFAM_BASEURL_KEY, "http://rfam.xfam.org");
+ url = new RfamSeed().getURL(" abc ");
+ assertEquals(url, "http://" + path);
+ }
+}
@Test(groups = { "External" })
public void testPfamFullAndSeed() throws Exception
{
- PfamFull pff = new PfamFull();
+ Pfam pff = new PfamFull();
PfamSeed pfseed = new PfamSeed();
AlignmentI fullpf = pff.getSequenceRecords(pff.getTestQuery());
@BeforeTest(alwaysRun = true)
public void populateExpectedMapping() throws SiftsException
{
- expectedMapping.put(51, new int[] { 1, 2 });
- expectedMapping.put(52, new int[] { 2, 7 });
- expectedMapping.put(53, new int[] { 3, 12 });
- expectedMapping.put(54, new int[] { 4, 24 });
- expectedMapping.put(55, new int[] { 5, 33 });
- expectedMapping.put(56, new int[] { 6, 40 });
- expectedMapping.put(57, new int[] { 7, 47 });
- expectedMapping.put(58, new int[] { 8, 55 });
- expectedMapping.put(59, new int[] { 9, 62 });
- expectedMapping.put(60, new int[] { 10, 69 });
- expectedMapping.put(61, new int[] { 11, 76 });
- expectedMapping.put(62, new int[] { 12, 83 });
- expectedMapping.put(63, new int[] { 13, 87 });
- expectedMapping.put(64, new int[] { 14, 95 });
- expectedMapping.put(65, new int[] { 15, 102 });
- expectedMapping.put(66, new int[] { 16, 111 });
- expectedMapping.put(67, new int[] { 17, 122 });
- expectedMapping.put(68, new int[] { 18, 131 });
- expectedMapping.put(69, new int[] { 19, 137 });
- expectedMapping.put(70, new int[] { 20, 144 });
- expectedMapping.put(71, new int[] { 21, 152 });
- expectedMapping.put(72, new int[] { 22, 160 });
- expectedMapping.put(73, new int[] { 23, 167 });
- expectedMapping.put(74, new int[] { 24, 179 });
- expectedMapping.put(75, new int[] { 25, 187 });
- expectedMapping.put(76, new int[] { 26, 195 });
- expectedMapping.put(77, new int[] { 27, 203 });
- expectedMapping.put(78, new int[] { 28, 208 });
- expectedMapping.put(79, new int[] { 29, 213 });
- expectedMapping.put(80, new int[] { 30, 222 });
- expectedMapping.put(81, new int[] { 31, 231 });
- expectedMapping.put(82, new int[] { 32, 240 });
- expectedMapping.put(83, new int[] { 33, 244 });
- expectedMapping.put(84, new int[] { 34, 252 });
- expectedMapping.put(85, new int[] { 35, 260 });
- expectedMapping.put(86, new int[] { 36, 268 });
- expectedMapping.put(87, new int[] { 37, 275 });
- expectedMapping.put(88, new int[] { 38, 287 });
- expectedMapping.put(89, new int[] { 39, 293 });
- expectedMapping.put(90, new int[] { 40, 299 });
- expectedMapping.put(91, new int[] { 41, 310 });
- expectedMapping.put(92, new int[] { 42, 315 });
- expectedMapping.put(93, new int[] { 43, 319 });
- expectedMapping.put(94, new int[] { 44, 325 });
- expectedMapping.put(95, new int[] { 45, 331 });
- expectedMapping.put(96, new int[] { 46, 337 });
- expectedMapping.put(97, new int[] { 47, 343 });
- expectedMapping.put(98, new int[] { 48, 349 });
- expectedMapping.put(99, new int[] { 49, 354 });
- expectedMapping.put(100, new int[] { 50, 358 });
- expectedMapping.put(101, new int[] { 51, 367 });
- expectedMapping.put(102, new int[] { 52, 375 });
- expectedMapping.put(103, new int[] { 53, 384 });
- expectedMapping.put(104, new int[] { 54, 391 });
- expectedMapping.put(105, new int[] { 55, 395 });
- expectedMapping.put(106, new int[] { 56, 401 });
- expectedMapping.put(107, new int[] { 57, 409 });
- expectedMapping.put(108, new int[] { 58, 417 });
- expectedMapping.put(109, new int[] { 59, 426 });
- expectedMapping.put(110, new int[] { 60, 434 });
- expectedMapping.put(111, new int[] { 61, 442 });
- expectedMapping.put(112, new int[] { 62, 451 });
- expectedMapping.put(113, new int[] { 63, 457 });
- expectedMapping.put(114, new int[] { 64, 468 });
- expectedMapping.put(115, new int[] { 65, 476 });
- expectedMapping.put(116, new int[] { 66, 484 });
- expectedMapping.put(117, new int[] { 67, 492 });
- expectedMapping.put(118, new int[] { 68, 500 });
- expectedMapping.put(119, new int[] { 69, 509 });
- expectedMapping.put(120, new int[] { 70, 517 });
- expectedMapping.put(121, new int[] { 71, 525 });
- expectedMapping.put(122, new int[] { 72, 534 });
- expectedMapping.put(123, new int[] { 73, 538 });
- expectedMapping.put(124, new int[] { 74, 552 });
- expectedMapping.put(125, new int[] { 75, 559 });
- expectedMapping.put(126, new int[] { 76, 567 });
- expectedMapping.put(127, new int[] { 77, 574 });
- expectedMapping.put(128, new int[] { 78, 580 });
- expectedMapping.put(129, new int[] { 79, 585 });
- expectedMapping.put(130, new int[] { 80, 590 });
- expectedMapping.put(131, new int[] { 81, 602 });
- expectedMapping.put(132, new int[] { 82, 609 });
- expectedMapping.put(133, new int[] { 83, 616 });
- expectedMapping.put(134, new int[] { 84, 622 });
- expectedMapping.put(135, new int[] { 85, 630 });
- expectedMapping.put(136, new int[] { 86, 637 });
- expectedMapping.put(137, new int[] { 87, 644 });
- expectedMapping.put(138, new int[] { 88, 652 });
- expectedMapping.put(139, new int[] { 89, 661 });
- expectedMapping.put(140, new int[] { 90, 668 });
- expectedMapping.put(141, new int[] { 91, 678 });
- expectedMapping.put(142, new int[] { 92, 687 });
- expectedMapping.put(143, new int[] { 93, 696 });
- expectedMapping.put(144, new int[] { 94, 705 });
- expectedMapping.put(145, new int[] { 95, 714 });
- expectedMapping.put(146, new int[] { 96, 722 });
- expectedMapping.put(147, new int[] { 97, 729 });
+ expectedMapping.put(51, new int[] { 1, 2, 1 });
+ expectedMapping.put(52, new int[] { 2, 7, 2 });
+ expectedMapping.put(53, new int[] { 3, 12, 3 });
+ expectedMapping.put(54, new int[] { 4, 24, 4 });
+ expectedMapping.put(55, new int[] { 5, 33, 5 });
+ expectedMapping.put(56, new int[] { 6, 40, 6 });
+ expectedMapping.put(57, new int[] { 7, 47, 7 });
+ expectedMapping.put(58, new int[] { 8, 55, 8 });
+ expectedMapping.put(59, new int[] { 9, 62, 9 });
+ expectedMapping.put(60, new int[] { 10, 69, 10 });
+ expectedMapping.put(61, new int[] { 11, 76, 11 });
+ expectedMapping.put(62, new int[] { 12, 83, 12 });
+ expectedMapping.put(63, new int[] { 13, 87, 13 });
+ expectedMapping.put(64, new int[] { 14, 95, 14 });
+ expectedMapping.put(65, new int[] { 15, 102, 15 });
+ expectedMapping.put(66, new int[] { 16, 111, 16 });
+ expectedMapping.put(67, new int[] { 17, 122, 17 });
+ expectedMapping.put(68, new int[] { 18, 131, 18 });
+ expectedMapping.put(69, new int[] { 19, 137, 19 });
+ expectedMapping.put(70, new int[] { 20, 144, 20 });
+ expectedMapping.put(71, new int[] { 21, 152, 21 });
+ expectedMapping.put(72, new int[] { 22, 160, 22 });
+ expectedMapping.put(73, new int[] { 23, 167, 23 });
+ expectedMapping.put(74, new int[] { 24, 179, 24 });
+ expectedMapping.put(75, new int[] { 25, 187, 25 });
+ expectedMapping.put(76, new int[] { 26, 195, 26 });
+ expectedMapping.put(77, new int[] { 27, 203, 27 });
+ expectedMapping.put(78, new int[] { 28, 208, 28 });
+ expectedMapping.put(79, new int[] { 29, 213, 29 });
+ expectedMapping.put(80, new int[] { 30, 222, 30 });
+ expectedMapping.put(81, new int[] { 31, 231, 31 });
+ expectedMapping.put(82, new int[] { 32, 240, 32 });
+ expectedMapping.put(83, new int[] { 33, 244, 33 });
+ expectedMapping.put(84, new int[] { 34, 252, 34 });
+ expectedMapping.put(85, new int[] { 35, 260, 35 });
+ expectedMapping.put(86, new int[] { 36, 268, 36 });
+ expectedMapping.put(87, new int[] { 37, 275, 37 });
+ expectedMapping.put(88, new int[] { 38, 287, 38 });
+ expectedMapping.put(89, new int[] { 39, 293, 39 });
+ expectedMapping.put(90, new int[] { 40, 299, 40 });
+ expectedMapping.put(91, new int[] { 41, 310, 41 });
+ expectedMapping.put(92, new int[] { 42, 315, 42 });
+ expectedMapping.put(93, new int[] { 43, 319, 43 });
+ expectedMapping.put(94, new int[] { 44, 325, 44 });
+ expectedMapping.put(95, new int[] { 45, 331, 45 });
+ expectedMapping.put(96, new int[] { 46, 337, 46 });
+ expectedMapping.put(97, new int[] { 47, 343, 47 });
+ expectedMapping.put(98, new int[] { 48, 349, 48 });
+ expectedMapping.put(99, new int[] { 49, 354, 49 });
+ expectedMapping.put(100, new int[] { 50, 358, 50 });
+ expectedMapping.put(101, new int[] { 51, 367, 51 });
+ expectedMapping.put(102, new int[] { 52, 375, 52 });
+ expectedMapping.put(103, new int[] { 53, 384, 53 });
+ expectedMapping.put(104, new int[] { 54, 391, 54 });
+ expectedMapping.put(105, new int[] { 55, 395, 55 });
+ expectedMapping.put(106, new int[] { 56, 401, 56 });
+ expectedMapping.put(107, new int[] { 57, 409, 57 });
+ expectedMapping.put(108, new int[] { 58, 417, 58 });
+ expectedMapping.put(109, new int[] { 59, 426, 59 });
+ expectedMapping.put(110, new int[] { 60, 434, 60 });
+ expectedMapping.put(111, new int[] { 61, 442, 61 });
+ expectedMapping.put(112, new int[] { 62, 451, 62 });
+ expectedMapping.put(113, new int[] { 63, 457, 63 });
+ expectedMapping.put(114, new int[] { 64, 468, 64 });
+ expectedMapping.put(115, new int[] { 65, 476, 65 });
+ expectedMapping.put(116, new int[] { 66, 484, 66 });
+ expectedMapping.put(117, new int[] { 67, 492, 67 });
+ expectedMapping.put(118, new int[] { 68, 500, 68 });
+ expectedMapping.put(119, new int[] { 69, 509, 69 });
+ expectedMapping.put(120, new int[] { 70, 517, 70 });
+ expectedMapping.put(121, new int[] { 71, 525, 71 });
+ expectedMapping.put(122, new int[] { 72, 534, 72 });
+ expectedMapping.put(123, new int[] { 73, 538, 73 });
+ expectedMapping.put(124, new int[] { 74, 552, 74 });
+ expectedMapping.put(125, new int[] { 75, 559, 75 });
+ expectedMapping.put(126, new int[] { 76, 567, 76 });
+ expectedMapping.put(127, new int[] { 77, 574, 77 });
+ expectedMapping.put(128, new int[] { 78, 580, 78 });
+ expectedMapping.put(129, new int[] { 79, 585, 79 });
+ expectedMapping.put(130, new int[] { 80, 590, 80 });
+ expectedMapping.put(131, new int[] { 81, 602, 81 });
+ expectedMapping.put(132, new int[] { 82, 609, 82 });
+ expectedMapping.put(133, new int[] { 83, 616, 83 });
+ expectedMapping.put(134, new int[] { 84, 622, 84 });
+ expectedMapping.put(135, new int[] { 85, 630, 85 });
+ expectedMapping.put(136, new int[] { 86, 637, 86 });
+ expectedMapping.put(137, new int[] { 87, 644, 87 });
+ expectedMapping.put(138, new int[] { 88, 652, 88 });
+ expectedMapping.put(139, new int[] { 89, 661, 89 });
+ expectedMapping.put(140, new int[] { 90, 668, 90 });
+ expectedMapping.put(141, new int[] { 91, 678, 91 });
+ expectedMapping.put(142, new int[] { 92, 687, 92 });
+ expectedMapping.put(143, new int[] { 93, 696, 93 });
+ expectedMapping.put(144, new int[] { 94, 705, 94 });
+ expectedMapping.put(145, new int[] { 95, 714, 95 });
+ expectedMapping.put(146, new int[] { 96, 722, 96 });
+ expectedMapping.put(147, new int[] { 97, 729, 97 });
}
@BeforeTest(alwaysRun = true)
atom.atomIndex = 7;
atoms.add(atom);
int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
- Assert.assertEquals(actualAtomIndex, -1);
+ Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED);
actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
Assert.assertEquals(actualAtomIndex, 7);
}
git://source.jalview.org / jalview.git / commitdiff