Add observed ion mobility and CCS to chromatogram extraction

pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs

@@ -357,7 +357,7 @@ private string SetTmpDirForCleanup(ProcessStartInfo psi)
                         exeName = Path.GetFileNameWithoutExtension(psi.FileName);
                         if (!string.IsNullOrEmpty(exeName))
                         {
-                            tmpDirForCleanup = Path.Combine(tmpDirForCleanup, exeName + "_" + Path.GetRandomFileName());
+                            tmpDirForCleanup = Path.Combine(tmpDirForCleanup, exeName + @"_" + Path.GetRandomFileName());
                         }
                     }
 

pwiz_tools/Skyline/Controls/Graphs/GraphsResources.resx

@@ -553,6 +553,25 @@ Here are the last 3 errors:
   <data name="GraphFullScan_ToolTip_Summed_Intensity" xml:space="preserve">
     <value>Summed Intensity</value>
   </data>
+  <data name="GraphFullScan_ToolTip_IonMobilityFilterHeader" xml:space="preserve">
+    <value>Ion Mobility Filter</value>
+    <comment>Header for the tooltip on the dashed target-IM line; the body rows show the filter's IM, CCS, and isolation window for the current target.</comment>
+  </data>
+  <data name="GraphFullScan_ToolTip_IsolationWindow" xml:space="preserve">
+    <value>Isolation Window</value>
+  </data>
+  <data name="GraphFullScan_ToolTip_ObservedAtPeakHeaderFormat" xml:space="preserve">
+    <value>Observed at Peak (RT={0})</value>
+    <comment>{0} = peak retention time. Header row for the observed-line tooltip; subsequent rows show IM and CCS values.</comment>
+  </data>
+  <data name="GraphFullScan_ToolTip_Ccs" xml:space="preserve">
+    <value>CCS</value>
+    <comment>Compact column name used in the observed-line tooltip under the "Observed at Peak" header.</comment>
+  </data>
+  <data name="GraphFullScan_ToolTip_ObservedValueWithErrorFormat" xml:space="preserve">
+    <value>{0} ({1}% error)</value>
+    <comment>{0} = numeric value, {1} = percent error vs target. Used inline in the observed-line tooltip rows.</comment>
+  </data>
   <data name="GraphSpectrum_DoUpdate_dotp___0_0_0000_" xml:space="preserve">
     <value>{0:0.0000}</value>
   </data>

pwiz_tools/Skyline/Controls/NodeTip.cs

@@ -358,6 +358,19 @@ public void AddDetailRowNoBold(string name, string value, RenderTools rt)
             AddDetailRow(name, value, rt, StringAlignment.Near, rt.FontNormal, rt.FontNormal);
         }
 
+        /// <summary>
+        /// Adds a single-cell row marked as a header. Header rows are NOT included
+        /// in the per-column width calculation, so a long header doesn't widen the
+        /// following data rows' first column. Render uses the full table width.
+        /// </summary>
+        public void AddHeaderRow(string text, RenderTools rt, Font font = null)
+        {
+            var row = new RowDesc { IsHeader = true };
+            row.Add(new CellDesc(text, rt) { Font = font ?? rt.FontBold });
+            row.ColumnSpacing = COL_SPACING;
+            Add(row);
+        }
+
         private const string X80 =
             @"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";
 
@@ -407,15 +420,25 @@ public SizeF CalcDimensions(Graphics g)
                 float heightMax = 0f;
 
                 row.CalcDimensions(g);
-                for (int i = 0; i < row.Count; i++)
+                // Header rows are full-width: their text size doesn't contribute
+                // to column widths, but their height still grows the table.
+                if (!row.IsHeader)
+                {
+                    for (int i = 0; i < row.Count; i++)
+                    {
+                        if (i == colWidths.Count)
+                            colWidths.Add(0f);
+                        SizeF sizeCell = row[i].SizeF;
+                        colWidths[i] = Math.Max(colWidths[i], sizeCell.Width);
+                        // Add spacing, if this is not the last column
+                        colWidths[i] += i < row.Count - 1 ? row.ColumnSpacing : 1;
+                        heightMax = Math.Max(heightMax, sizeCell.Height);
+                    }
+                }
+                else
                 {
-                    if (i == colWidths.Count)
-                        colWidths.Add(0f);
-                    SizeF sizeCell = row[i].SizeF;
-                    colWidths[i] = Math.Max(colWidths[i], sizeCell.Width);
-                    // Add spacing, if this is not the last column
-                    colWidths[i] += i < row.Count - 1 ? row.ColumnSpacing : 1;
-                    heightMax = Math.Max(heightMax, sizeCell.Height);
+                    foreach (CellDesc cell in row)
+                        heightMax = Math.Max(heightMax, cell.SizeF.Height);
                 }
 
                 // Reset the heights all to the same value
@@ -425,17 +448,36 @@ public SizeF CalcDimensions(Graphics g)
                 size.Height += heightMax;
             }
 
+            // Total the widths used. Header rows may push the table wider if
+            // the header text is longer than all data rows combined.
+            float dataTotalWidth = 0;
+            foreach (float width in colWidths)
+                dataTotalWidth += width;
+            float maxHeaderWidth = 0;
             foreach (RowDesc row in this)
             {
-                // Reset widths for each column to the same value
-                for (int i = 0; i < row.Count; i++)
-                    row[i].Width = colWidths[i];
+                if (row.IsHeader && row.Count > 0 && row[0].SizeF.Width > maxHeaderWidth)
+                    maxHeaderWidth = row[0].SizeF.Width;
             }
+            float tableWidth = Math.Max(dataTotalWidth, maxHeaderWidth);
 
-            // Total the widths used.
-            foreach (float width in colWidths)
-                size.Width += width;
+            foreach (RowDesc row in this)
+            {
+                if (row.IsHeader)
+                {
+                    // Header gets the full table width in its single cell.
+                    if (row.Count > 0)
+                        row[0].Width = tableWidth;
+                }
+                else
+                {
+                    // Reset widths for each column to the same value
+                    for (int i = 0; i < row.Count; i++)
+                        row[i].Width = colWidths[i];
+                }
+            }
 
+            size.Width += tableWidth;
             return size;
         }
 
@@ -470,6 +512,11 @@ public class RowDesc : List<CellDesc>
     {
         public int ColumnSpacing { get; set; }
 
+        // Header rows render as a single full-width cell and do NOT participate
+        // in the table's per-column width calculation. A long header therefore
+        // doesn't push the following data rows' columns to the right.
+        public bool IsHeader { get; set; }
+
         public void CalcDimensions(Graphics g)
         {
             foreach (CellDesc cell in this)

pwiz_tools/Skyline/Documentation/Help/en/Reports-mixed.html

@@ -730,6 +730,10 @@
 <tr><td class="ColumnCaption">Height</td><td class="ColumnDescription">The maximum intensity of the points between the transition peak integration
 boundaries.</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Mass Error PPM</td><td class="ColumnDescription">The difference between the expected and measured m/z values expressed in parts per million (PPM)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed Ion Mobility</td><td class="ColumnDescription">Intensity-weighted ion mobility centroid across the peak, in the same units as the IM extraction filter.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed CCS</td><td class="ColumnDescription">Collision cross section in square Angstroms, computed from the observed ion mobility using the source instrument&#39;s vendor-supplied conversion. Available only for vendor formats that expose this conversion; open formats such as mzML and mz5 will leave this blank.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Ion Mobility Error Percent</td><td class="ColumnDescription">The difference between the expected and measured ion mobility values expressed as a percent of the expected value (intensity-weighted across the peak)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">CCS Error Percent</td><td class="ColumnDescription">The difference between the expected and measured collisional cross section (CCS) values expressed as a percent of the expected value</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Truncated</td><td class="ColumnDescription">True if the integrate peak has a boundary at either end of the acquisition
 time range, where intensity at the end is greater than 25% of the background-subtracted peak height
 higher than the other extent.</td><td class="ColumnType">Boolean</td></tr>

pwiz_tools/Skyline/Documentation/Help/en/Reports-proteomic.html

@@ -723,6 +723,10 @@
 <tr><td class="ColumnCaption">Height</td><td class="ColumnDescription">The maximum intensity of the points between the transition peak integration
 boundaries.</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Mass Error PPM</td><td class="ColumnDescription">The difference between the expected and measured m/z values expressed in parts per million (PPM)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed Ion Mobility</td><td class="ColumnDescription">Intensity-weighted ion mobility centroid across the peak, in the same units as the IM extraction filter.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed CCS</td><td class="ColumnDescription">Collision cross section in square Angstroms, computed from the observed ion mobility using the source instrument&#39;s vendor-supplied conversion. Available only for vendor formats that expose this conversion; open formats such as mzML and mz5 will leave this blank.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Ion Mobility Error Percent</td><td class="ColumnDescription">The difference between the expected and measured ion mobility values expressed as a percent of the expected value (intensity-weighted across the peak)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">CCS Error Percent</td><td class="ColumnDescription">The difference between the expected and measured collisional cross section (CCS) values expressed as a percent of the expected value</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Truncated</td><td class="ColumnDescription">True if the integrate peak has a boundary at either end of the acquisition
 time range, where intensity at the end is greater than 25% of the background-subtracted peak height
 higher than the other extent.</td><td class="ColumnType">Boolean</td></tr>

pwiz_tools/Skyline/Documentation/Help/en/Reports-small_molecules.html

@@ -679,6 +679,10 @@
 <tr><td class="ColumnCaption">Height</td><td class="ColumnDescription">The maximum intensity of the points between the transition peak integration
 boundaries.</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Mass Error PPM</td><td class="ColumnDescription">The difference between the expected and measured m/z values expressed in parts per million (PPM)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed Ion Mobility</td><td class="ColumnDescription">Intensity-weighted ion mobility centroid across the peak, in the same units as the IM extraction filter.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed CCS</td><td class="ColumnDescription">Collision cross section in square Angstroms, computed from the observed ion mobility using the source instrument&#39;s vendor-supplied conversion. Available only for vendor formats that expose this conversion; open formats such as mzML and mz5 will leave this blank.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Ion Mobility Error Percent</td><td class="ColumnDescription">The difference between the expected and measured ion mobility values expressed as a percent of the expected value (intensity-weighted across the peak)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">CCS Error Percent</td><td class="ColumnDescription">The difference between the expected and measured collisional cross section (CCS) values expressed as a percent of the expected value</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">Truncated</td><td class="ColumnDescription">True if the integrate peak has a boundary at either end of the acquisition
 time range, where intensity at the end is greater than 25% of the background-subtracted peak height
 higher than the other extent.</td><td class="ColumnType">Boolean</td></tr>

pwiz_tools/Skyline/Documentation/Help/ja/Reports-mixed.html

@@ -640,6 +640,10 @@
 <tr><td class="ColumnCaption">面積の正規化</td><td class="ColumnDescription">ドキュメント内の全トランジションのArea値合計に対して正規化された Areaです。</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">高さ</td><td class="ColumnDescription">トランジションピークの積分境界の間の点の最大強度です。</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">質量誤差PPM</td><td class="ColumnDescription">期待値と測定値のm/z値の差を百万分率（PPM）で表示</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed Ion Mobility</td><td class="ColumnDescription">Intensity-weighted ion mobility centroid across the peak, in the same units as the IM extraction filter.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Observed CCS</td><td class="ColumnDescription">Collision cross section in square Angstroms, computed from the observed ion mobility using the source instrument&#39;s vendor-supplied conversion. Available only for vendor formats that expose this conversion; open formats such as mzML and mz5 will leave this blank.</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">Ion Mobility Error Percent</td><td class="ColumnDescription">The difference between the expected and measured ion mobility values expressed as a percent of the expected value (intensity-weighted across the peak)</td><td class="ColumnType">Double</td></tr>
+<tr><td class="ColumnCaption">CCS Error Percent</td><td class="ColumnDescription">The difference between the expected and measured collisional cross section (CCS) values expressed as a percent of the expected value</td><td class="ColumnType">Double</td></tr>
 <tr><td class="ColumnCaption">切断</td><td class="ColumnDescription">積分ピークの境界がデータ取得時間幅のいずれかの終端にあり、その終端がもう一方の終端よりもバックグラウンドを差し引いたピーク高さが25%以上高い場合は真となります。</td><td class="ColumnType">Boolean</td></tr>
 <tr><td class="ColumnCaption">ピークのランク</td><td class="ColumnDescription">同じプリカーサーのその他すべてのトランジションの中での、このトランジションの Areaに基づく順位です。</td><td class="ColumnType">Int32</td></tr>
 <tr><td class="ColumnCaption">レベル別のピークのランク</td><td class="ColumnDescription">MSレベルによる特定の繰り返し測定におけるピーク面積順位付け（MS1とMS/MSの順位付けは別になります）</td><td class="ColumnType">Int32</td></tr>